This practice isn't just restricted to Japanese entertainment, although it is indeed particularly common there.
Still, the practice, which I call using "fakemarks" (the term is not in wide usage and if there is a widely accepted word for it I don't know what it is) is widespread in popular culture fiction both in and outside Japan. It is especially common among smaller scale producers of fiction worldwide.
I actually keep a portfolio of screen shots of them for use in teaching materials about trademarks and about popular culture. Here are a few examples of typical "fakemarks" from "the wild":
It is intended to and does successfully serve the purpose of discouraging trademark infringement lawsuits by showing non-affiliation with the trademark owner which makes it non-infringing. You also see it more in a lot of non-U.S. and non-Japanese popular culture (e.g. in works made in Indonesia and Turkey), and in U.S. works made by small independent creative producers (like webcomic artists and people writing graphic novels or online fiction who aren't affiliated with D.C. or Marvel or a major publishing firm).
People use fakemarks to the extent that they do, mostly because they believe that the scope of trademark infringement is broader than it really is (a concern that regularly comes up in Law.SE questions), combined with an aversion to the risk associated with being in a gray area and incurring legal fees even if you win. This aversion has sparked industry norms and tropes such as the ones you describe.
The greater aversion to risk of trademark infringement in Japan than in the U.S., that gave rise to these industry conventions and norms, has a lot to do with the way the respective popular culture industries are organized economically.
The Economic Organization Of Anime and Manga In Japan
Japanese anime films (where you see fakemarks used a lot) are a very intimately related direct outgrowth of the Japanese manga industry (i.e. Japanese graphic novels), with the core creative decisions like those that give rise to fakemark use made at the stage of the production of the source manga. A very large share of TV series anime are adaptations of manga that have been adapted for animated format, although there are a few exceptions producing original work, like Studio Ghibli that notably are less prone to use fakemarks. In the early days of anime, often lengthy shots of the animation were created by just a camera creating the illusion of movement by panning around a still manga illustration to save time and money.
The manga industry in Japan is very highly decentralized, despite being highly profitable for the top manga writers (who are called "mangaka"). Many of the people with the highest annual personal incomes in Japan according to public tax collection agency statistics, are mangaka, in part, because mangaka are self-employed and often paid a percentage royalty, and in part, because corporate executives in Japan are paid much lower salaries directly than comparable executives in the U.S. and accumulate a lot of their wealth in the form of highly indirectly held ownership interests in business conglomerates, often acquired as founders or inheritors, that they hold for long periods of time without generating taxable income.
But, while the top mangaka make huge bank when their works are selling well, the names at the top shift frequently and there is a long tail of mangaka who currently squeeze buy with just barely enough money from one or two serializations or commissioned works (like illustrated safety manuals and handbooks) to pay their bills hoping to get lucky and make it big someday.
A typical manga is produced by one or two main authors (sometimes the drawing and the story/dialog are split between two people and sometimes one person does both), supplemented by one to a few assistants artists who often work either in the home of the artist or remotely from their own homes, who do finishing work like reinforcing line work, backgrounds, shading, and coloring. Sometimes there would be a copy editor and/or an assistant who writes in the dialog and text.
Mangaka are generally independent contractors, often operating as sole proprietors. They typically submit their works to magazines as freelancers with only a light editorial role. The magazine editor working with a freelance mangaka's work usually consists mostly of working with prospective freelance mangaka to approve a new series, hounding their contracted mangaka to get work in by the magazine's rigid publication process driven deadlines, and deciding when a series has lost popularity and needs to be shut down. Often, the mangaka will retain the right to republish the originally serialized manga in multi-volume book form with another publisher (although, of course, contract terms vary).
So, mangaka typically don't have access to lawyers, and the main kind of lawyer that they would refer to for intellectual property advice in Japan are scarce, more similar to English barristers than to U.S. attorneys, and very expensive to hire for a consult. There are only about 14,000 lawyers in private practice in all of Japan (which on a per capita basis would be comparable to the U.S. having about 36,000 lawyers), only a minority of whom would handle matters like advising someone on the impact of trademark law on their creative manga writing decisions. The U.S., in contrast, has about 1,300,000 lawyers, which is about 36 times as many per capita.
As noted before, once a manga is green lit to become an anime, the key creative decisions that might benefit from legal consults have already been made, so the anime production company that can afford to hire them doesn't provide input on those issues.
Also, while manga artists often do go to art school, the typical art school curricula in Japan includes much less instruction on the business and legal side of working as a creative professional than comparable courses of instruction in the U.S. would.
The Economic Organization Of Popular Culture In The U.S.
In contrast, in the U.S., lots of popular culture for the mass market, like television shows are much larger operations and even when they are adapted from books, are much less direct and faithful adaptation (often only "inspired by" the source material).
U.S. productions, in part, because they are more likely to be live action and filmed on location, are often initiated by corporate executive type people called producers rather than by screenwriters or book authors, and a typical production as you know if you have ever watched the credits of a TV show, may have hundreds of employees and contracting companies, separate companies formed for the purpose of the show. The credits of a U.S. TV series or movie invariably has a general counsel lawyer and frequently an associate attorney or two on the payroll, as part of the group of people producing the work.
Even comics and books in the U.S. are published by firms that are much more "corporate" at the creative design phase of the work, than a mangaka's home office and band of assistants and apprentices. And, as expensive as they are, it is much more economically feasible for the producers of a U.S. popular culture production or the publishers of a comic or book in the U.S. to make legal counsel available to the people doing the creative work to advise on issues like trademark infringement.
Trademark lawyers in the U.S. aren't cheap, but they are less expensive than comparable Japanese lawyers and the economics of U.S. popular culture production make these lawyers more available to people who need to utilize their services while engaged in the creative production process for popular culture works in the U.S.
As a result, U.S. popular culture producers at the high end of that the industry in terms of economic scale (which is where much more of it is located at the creative design stage), being better informed about trademark law. As a result the U.S. industry has not had to be as cautious and is in a better position to get closer to the line of what constitutes permissible nominative use of trademarks than the people who make Japanese manga and anime.
Another issue is that business minded producers of U.S. popular culture works often use product placement as a separate revenue stream or as a way to finance set, costume and prop elements for their works, by agreement with the trademark holder, something that is typically not a viable option for a lonely mangaka who has not yet made it big.
Counterexamples To Intellectual Property Conservatism In Japan
This said, industry norms do not always work in the direction of caution in Japan, and those norms do influence what is considered to be fair use in copyright in Japan.
For example, Japanese mangaka are more comfortable with using highly referenced illustrations that sometimes even depict copyrighted works when they are not trademarks or trade names, than U.S. popular culture producers.
This is, in part, because when you are drawing everything, rather than filming, in the original story source material, at least historically, the time savings for a small shop operation using highly referenced illustrations are immense, and because it helps mangaka meet the externally imposed and strict deadlines imposed by the magazines that serialize them.
Footnote On Sourcing
I read quite a bit of manga, watch quite a bit of anime, and in general consume quite a bit of non-U.S. popular culture. As a lawyer, I'm naturally also interested in learning about the economics and law behind these forms of entertainment. And, it is customary in manga to periodically break the fourth wall and have the author discuss their personal lives and work process after every few chapters of their fictional works. Between this, and a few mini-features on the subject, and a reading a few law review articles on copyright enforcement for fan fiction, I've developed some familiarity with the organization of the entertainment industry in Japan, in the U.S., and in some other countries. But, I'd be hard pressed to reference those sources with hyperlinks or citations, because this is knowledge that I've accumulated on a fragmentary basis over decades and didn't anticipate at the time I was encountering most of it that I'd ever need to be able to refer back to and cite to it.