It’s a small thing that I think Flatpak is really missing. Drag and drop should just work, regardless of the permissions of the app, but it doesn’t because what it feels like you are doing is different from what you are really doing doing. What you are really doing is simply pointing the app to where the files are that you want it to access, so I’m unsure how to fix that problem. I would love to see it fixed though, along with an open dialog that gives temporary permission to files.