it’s almost an entirely different OS that happens to run the same binaries

What?

As far as I know, it’s literally just an immutable build of Arch Linux.

Hopefully support for that will come through desktop portals.

Comparing Flatpak or Gnome to Apple seems highly irrelevant in the context of this post. But, you do realize that neither Gnome, nor Flatpak is a trillion dollar company, right? Also, since when are Flatpak apps “barely usable”?

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UEFI by default runs exe

As far as I know, that’s not the case. Maybe some UEFI implementations by some vendors can extract the UEFI firmware that’s embedded in the exe file. But, UEFI doesn’t run exe files.