[smoldesu]

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.