A 3" chop won't be that noticeable by many except, for us experienced stovebolters. There is room on the back of the cab the lower the rear window 3" thereby maintaining the full rear window and avoiding the "Mail Slot" tiny window.
If the truck suspension is also lowered then the chopped roof and lowered suspension will look balanced overall. An unchopped roof on an AD truck will give the appearance that it is actually taller that the stock roof if the suspension has been lowered. It's an optical illusion. I restore and modify AD trucks along with a friend of mine. I appreciate the stock restored look and the "hot rod" look if it's done tastefully. Good Luck with your project.