How do I remove the default tool settings, default gradients, default patterns...

[Ofnuts]

I think your best bet is to copy the ones you want to keep to your personal folder(s) and to use Preferences>Folders to remove the "system" folders (the one in /app in the list). This way if you update the flatpak the unwanted files won't come back.

Two ways to do this and still be able to tell what is Gimp and what is yours:

1. Copy the whole folder(s) to your user space, add it to the Gimp folders in Preferences, and then remove what you don't want.
   
2. Create empty folders in your user space, and add soft links to the few bits you still use in the flatpak.
   

In the flatpak application, flatpak contents appear in the /app virtual filesystem. Outside of the application, the files of the current Gimp version can be found at: /var/lib/flatpak/app/org.gimp.GIMP/current/active/files/share/gimp/2.0/