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For flatpak, the installed apps go to /var/lib/flatpak for system-wide, ~/.local/share/flatpak for user-specific.

Then there's the question of app-created data, that would normally go into some dot-directory. Flatpak by default redirects all XDG dirs into ~/.var/app/${appid}, but as a part of the required permissions, the apps can request access to the user homedir or specific subfolders.

Some apps abuse it. Yes, I do mind, when an app liters into ~/Documents/. I'm looking at you, Viber.

An /app isn't any better. If they insist on having a fully realized file-system, they can put it under /opt. Or, they could use symlinks to construct it under /run/{app,snap} similar to a chroot setup.

/app is not visible on the host system, only inside the container. It is chroot on steroids.

I don't mind that behavior.

/app is never visible on the host though