D’oh… I just uninstalled the flatpak and deleted that version of the config 
I should have taken some screenshots. I can reinstall it later and do that.
For now, here are descriptions of a few of the biggest issues I’ve run into with the flatpak which have (so far!) not occurred with the appimage:
- Cropping. When cropping an image, artifacts will sometimes appear in the resulting image. Most common this presents as white garbage around the edges, but sometimes I’ll get big ugly artifacts in the middle of the image as well. One guaranteed way to get this to happen was to: crop, then undo, then re-do. The artifacts weren’t just superficial either – when I “export” the image (to a png or whatever), the artifacts were present in the exported image as well. (I always saved before cropping for this reason, since restoring from a previous save was the only way I felt comfortable to “fix” this.)
- Opening a new file from the file manager. When Krita is already open, opening another
krafile from the file manager. Normally this simply opens the new file in a new tab of the existing window. But around half the time, this would attempt to open a new Krita window, which would simply hang indefinitely. After several minutes, an error dialog would appear. (EDIT: I see this has been a known issue for years now…) - Textured brushes. Sometimes textured brushes simply stopped working. The brushes themselves worked, but their texture would simply not appear. No amount of toggling brush options or changing things in that current Krita instance would fix this. Restarting Krita fixed it every time.
Those are the most egregious issues, but there may have been other smaller nits that I didn’t note down.
I know other folks have experienced issues as well. (Aside from the issues Deevad has mentioned in the past.) For example, I came across this thread recently when looking into these issues.
You can get some idea of past and present issues by looking at the issue list of the flatpak github page.