This is an inherent limitation of the way OSs are built. Linux, Windows, macOS are all like this. macOS is currently the furthest ahead in this since they're sharing code with iOS, but it's still not where it should be.

The Linux kernel is not at a point of allowing this kind of fine grained sandboxing or mocking of APIs. I'm guessing because it's a significant undertaking. I'm sure as more features become available in the Kernel w.r.t. sandboxing Snap and Flatpak will definitely utilise them.