Many employers demand that you use Microsoft's Windows or Apple's macOS if you want to work remotely from home even if they are not technical requirements. As a result this essentially amounts to discrimination against users of GNU/Linux. Should the freedom to choose your own Operating System (or other open source software alternatives) be protected in the same way as the right to choose your own religion. In many ways the two concepts are very similar. Serious GNU/Linux users tend to have a fanatical opinion about their choice of OS and quite often preach to others about the benefits while attempting to convert their peers.
Could the freedom to choose an Operating System be a legally enforceable basic human right?
No, meaning that accommodating the alleged needs that would benefit --at most-- a very narrow sector of the population is not worth enacting the fundamental amendments (possibly a cascade thereof) that this would entail.
I will focus on US law since you did not specify a jurisdiction. 42 U.S. § 2000e et seq list the categories that the Civil Rights Act protects: namely, race, color, religion, sex, and national origin. See, for instance, the multiple times these categories are mentioned in 42 U.S. § 2000e-2.
Of these protected categories, religion is the closest one to the issue of a person's hypothetical right to choice of OS. Indeed, religion is the only protected category that an individual is not born with (note, though, that Jews will disagree on this), and/or which one can adopt or switch based on the evolution of that individual's convictions.
But even if a person could persuasively argue that his adherence to some OS fits the elements of "religious observance, practice, or belief", discrimination on the basis of OS is not sanctionable because 42 U.S. § 2000e-2(j) provides for exemptions where
an employer demonstrates that he is unable to reasonably accommodate to an employee’s or prospective employee’s religious observance or practice without undue hardship on the conduct of the employer’s business.
In the context of choice of OS, the undue hardship is obvious from the additional costs a business would incur to ensure systems cross-compatibility, maintenance, dependence on more types of specialized staff, documentation that requires a greater degree of customization (or versioning, if you will), and so forth.
Furthermore, it is not that business would discriminate against an individual merely for being skilled in --passionate about-- Operating Systems other than those the company uses. It is just that the company has invested in certain equipment & software, and it accordingly needs personnel who is proficient to take advantage of that investment toward advancing the legitimate purpose of that business.