It would be nice to be able to, on third-party apps, use Proton Drive for things like backups, if the app supports it, but in a secure way.

The way it could work is that supported apps could have a "Connect to Proton Drive" button, and then you would be redirected to Proton to login and connect.

BUT, instead of giving apps access to all your Drive, each app would have its own folder, that the user can explore and edit if needed (with a new External apps menu in Drive, next to My Files, Computers, and Photos etc), where the user could also, when connecting, set a max folder size for the app (for example: app cant take more than 300mb on Drive), and the app could not see anything outside of that folder.
And the user could, in the Proton Drive settings, also have an External apps menu to edit the storage limit, or remove the connection with the external service at any moment.

I'l make an example with Aternos (the minecraft servers thing), which can currently backup servers to Google Drive, OneDrive, and Dropbox.

You would go into your Aternos settings, set Proton Drive as a backup method, login with your Proton account, choose or not choose a size limit, then an Aternos folder would be created on Drive, and the user could still go in there and see/edit files, and Aternos could not see anything inside the rest of Proton Drive.