This is kind of a shortcoming of all package management in general; should deleting the package delete your user data? There’s an argument to be made that data should be removed with the application, but deleting data irrecoverably as the default isn’t necessarily the easiest approach.

There’s also another problem, which is that the behaviour of deleting data may make sense for per-user applications, but for system-wide apps, should uninstalling an application start nuking data in people’s homedirs?

Because there are distros, like fedora for one, that have flat packs installable by the likes of discovery on KDE that doesn’t require CLI useage for install or uninstall of flatpacks

As far as I can tell this seems to be for deleting application data (~/.var/app/*), whereas flatpak uninstall --unused is for uninstalling runtimes that are no longer needed.

This app is more equivalent to flatpak uninstall --delete-data

No, that only deletes the leftover dependencies, it doesn’t delete any app data/config left over.