Building off this question, if a person is travelling with something that is for personal use that wouldn't be allowed across the border, would they be charged as if they were crossing the international border? Whereas they wouldn't have been searched if they were traveling elsewhere. Or more generally, what could they be charged with? Is it admissible if it had nothing to do with the border (e.g. something that generally comes from somewhere internally, far from the border)? There is the issue also of (state legal) cannabis transporters in southern California, it's not clear to me if they are charged when their goods are just seized at times. To be clear, internal checkpoints are treated like the real border, I'm just wondering the outcomes, i.e. charges.
would they be charged as if they were crossing the international border?
No. Or rather, maybe they would, but if the border patrol had no actual evidence of an actual border crossing then the prosecutor would probably decline to prosecute any such charges, the court would dismiss the charges, or the finder of fact would render a verdict of not guilty.
But there are plenty of charges available that don't include entry into the US as an element. There are laws against transporting illegal aliens within the US and there are laws against possessing cannabis within the US.
One thought experiment that serves to distinguish internal checkpoints from ports of entry is to think about less serious violations at ports of entry. If you buy something for $20,000 abroad, for example, you are supposed to declare it when you return to the US and pay customs duty. If you don't declare it and then they discover it during a search, you will suffer some negative consequences. But if you appear at a border checkpoint and they find a $20,000 necklace in your glove compartment, and you have a receipt showing that you just bought it (in the US), there is no violation.
People sometimes confuse the inland checkpoints with the "border search exception." The border search exception does not apply at internal immigration checkpoints. The border search exception allows customs agents to search you and your belongings when you're crossing an international border without any suspicion of a crime whatsoever. At an internal checkpoint, there has to be probable cause to search your vehicle (or consent).
You can read about drug-sniffing dogs being used at checkpoint stops to "manufacture" probable cause -- that is, the officer supposedly decides that it would be a good idea to search a car, but there are no circumstances that give probable cause, so they bring the dog and claim (perhaps falsely) that the dog has "alerted," indicating the presence of drugs in the vehicle. By contrast, you never read about this at the border, because at the border agents don't need probable cause to search vehicles. They use the dogs to help them to decide which vehicles to search and to help them find the things they're searching for.