Oh is that all? If you start writing up the requirements to make that happen (without permission prompts and portals, right?), I think you'll find that would be even more difficult than app isolation and have even more backward compatibility issues.
Can't imagine how per-app isolation would even work for me. Sounds like something inspired from android world where there's no such thing as having the same app run mutliple times on different workspaces/windows, etc. and the usability correspondingly suffers.
Portal thing even bit me recently. I leave dbus and window manager socket in the sandbox, so I can use GUI apps without too much trouble, and a few months back firefox started showing me files from outside the sandbox and hiding files in the sandbox in file save dialog, which confused the hell out of me, until I found out someone decided to add a remote file access via some dbus service or whatever. Dangerous. I had to remove dbus socket sharing completely from the sandbox at some inconvenience.