I would guess the RoI of refactoring (especially on a consumer OS) is pretty low though.

The average person never sees this stuff. Linux is widely used as a server OS and it still has taken a long time for new appraoches to get traction.

> I'd say that MacOS is even worse which is impressive given that Apple has the absolute control of the platform and seemingly infinite resources and could have refactored the mess at any point.

That's true, but also irrelevant. The file system can be a mess on MacOS because most MacOS users will never actually interact with the file system in any meaningful way. Apple obscures the file system away from its users by design. If you ask the average Mac user where on the computer their files are stored, they'll likely tell you something like, "They're all in the Photos app". On the other hand, even a fairly novice linux/unix user will almost certainly end up interacting with filesystem directly at some point, probably a lot.

And /Applications, and /System/Applications, even though if you open them in Finder, you'll see the two combined.