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.

Yeah, proper use of Flatpack requires antivirus, reverse firewall, hardware isolation (separate CPU core per application), user education, etc.

That's only true for the simplest of apps. The whole point of desktop OSs is that programs can integrate with each other, but that necessarily discards the notion of a sandbox almost entirely.

Yeah, e.g. file sandboxing approaches that work along the lines of "don't let the program access any files outside of its private directory except for those explicitly and lovingly hand-picked by the user" commonly ignore the existence of multi-file file formats.