I have to admit that I find the isolation and security design to be rather strange. Isolating graphical applications requires a lot of pieces, one of which (what Wayland did) is preventing them from poking at other applications via the GUI. It requires isolating them in the backend (out of scope for Wayland, but Flatpak is at least trying). But it also requires preventing them from spoofing each other and thus deliberately confusing the user. This seems like it needs UI enforced on top of the isolated applications, which means drawing them in a box (like a nested compositor, at which point none of what Wayland did to isolate applications matters) or enforcing informative window decorations. And that part seems like it requires server-side decorations, but Wayland is allergic to SSD.
So I don’t get it. How exactly is the core Wayland protocol a good base for the GUI parts of isolation?
You can render decorations server-side, it's just not guaranteed that the client will respect it. If you really want a Qubes-style SSD desktop, it's attainable in Wayland although it will look incredibly ugly and be highly redundant. Good luck pitching that to GNOME and KDE devs as a default.
So... I don't see how the isolation design is strange. Wayland makes sure that windows are individually isolated, and Flatpak/Bubblewrap isolates the backend and provides interaction portals. It's not a perfect solution, but it does stop your timer application from being a secret keylogger. If your biggest concern is a Trojan horse attack, it sounds to me like Wayland did what it set out to do.
So I don’t get it. How exactly is the core Wayland protocol a good base for the GUI parts of isolation?