If you want scanlines in fullscreen, the max resolution (as chosen in Mode) could be less than ideal.
Especially with the Crisp option checked, the 800x600 mode could be better.
As those pics illustrate (check them in full size). The 1280x1024 have some artefacts. It's because a fractional multiplier is used.
It really depends on your screen and video card.
1280x1024:
Check the bad artefacts
800x600:
Perfect!