pgcEdit: Options > Input/Output > Burn / Create ISO setup
will get you the burn setup screen.
I always cancel out of the Find BOVs window, since I'm not editing anything just making an ISO + layer break. I've never had that Verify... window but I'd try both and see how the ISO played via Daemon Tools or Alcohol 120%.
I've only ever seen a blue layer break twice, I normally pick one of the offered chapter breaks that has quiet audio or where a slight pause would not be too noticable. pgcEdit flags the chapter (cell) as seamless so modern players should play back with no pause.
Also, check your burner is up to burning DL, I upgraded an old LG to a cheap new Pioneer and went from 50/50 to 100% good burns.