if you designed the system so that the extension is part of the functionality, then you have to hide it away so that your users don’t accidentally delete or modify the extension thus rendering their files useless (within said system)
it’s a fundamental shell design flaw: one should never allow users to modify data critical to functionality. And it’s not something that can be changed because almost all applications depend on this
if we’re being fair, it did involve a lot of that historically. Package managers weren’t always around and even after they became established, there was still a lot of fiddling with bad drivers and various distributions had policies which didn’t allow certain software with certain licenses to be setup through their package repository and so on and so forth. Sure nowadays this is less of an issue, but then windows security is also much better than it used to be. People here seem to want to compare the latest Ubuntu to windows 98