I'm wondering about the tuning/nut issues you are experiencing on your SE DGT. I have an Paul's Guitar SE and the G string is sharp when fretting around the 2nd to 5th fret. I was thinking it could be an issue with the nut as well, though I've not attempted any changes yet.
I can push strings behind the nut and they go sharp and stay sharp. 4 out of 6 strings do that. It’s a nut issue not same as yours. The SE DGT frets are tall enough that I have to not squeeze as hard or I go sharp. The Paul’s guitar frets are not as tall but maybe you’re fretting too hard?