>With a permission model that apparently can't keep an image editing application from silently editing .bashrc .

It can, you can cut off all filesystem access or select certain areas. The problem is that programs often need special attention to make sure they work properly using flatpak portals. Currently not many devs are interested in doing this work since flatpak is pretty small right now.

So for now we must assume that Gimp built from the official source, is not a malicious program. Like we have for the last 25 years.