I prefer to have everything for one program in one place if possible... That's generally less confusing to me... (When things work that is).
But also because I never put anything in my account folder or documents folders. I'm not sure I want to start because sometime I might forget to backup stuff from those folders, but I guess I will start...

So I did the uninstall, then deleted everything that was left behind in Program Files and under AppData (I'm not sure the uninstaller removed anything under AppData at all), installed again with everything default (not clicking the button to have it install terrain data in the program directory), did 1 import to test, and it (correctly?) put things in the Outerra folder in my account folder. Nothing was installed under AppData.
Since it made the Jagerbomber folder under packages in the terrain data directory and not in the program directory, I use the terrain data directory for custom files and shouldn't touch the program directory at all?