Well, the ideal solution is to fix the application to use the special file chooser that gives the app permission to access whatever files the user chose. I only know the basics about Flatpak, but I know it has such a file chooser; does Gimp not use it, or is there some other issue that makes it require full home directory access?

In the meantime – sure, package the app, but it shouldn’t show up as “sandboxed” in the GUI if the sandbox isn’t meaningful. Instead it should come with a nice scary warning that the app has access to all of your files… you know, for everyone to ignore and click through. (You can lead a horse to water…)