I think it would be interesting if the file servers had read/write/list/delete permissions on files. For both groups and users.

It would mean the public stuff could see your files but private projects could exist. Eg. Maybe I don't want my At Protocol version of Figma making all my drawings public. If they could be shared in a group (anyone in a list in that folder or whatever).

Maybe this is coming, but would interest me way more about using applications on the atmosphere.

The ability to make information private fundamentally conflicts with how ATProto is designed. All records have to be sent to all Relays and AppView nodes on the network to provide a "global view" of the network. So there's no way to keep records private without locking out some user's servers from viewing them, and since AppViews are centralized indexing services, they won't function without being able to see the entire network.