yeah if + and - are the same as the advantage (furthest left and right on the numrow). I could see how that might cause an issue. If I ever have had that problem I've mostly gotten over that. That said, I don't often actually code on a normal keyboard so +/= and -/_ aren't really something that I'm using much. Any time I'm away from my desk it's often taking notes or responding to emails or slack .. so less technical things.
Just to say in my experience once you've fully settled into the advantage, and maybe this is just because I use an advantage and i've got the extra little 'hint' to my brain from the keywell shape, moving back and forth to flat boards doesn't cause any issues. I'm not missing keys because of the stagger differences, which I think was the primary concern.
The only things I keep on a separate layer are some multimodified keys that I use for window management, the f-row, and random things like keyboard backlight and bluetooth stuff, and a few macros.