Just my two cents here as an airline pilot myself:
Any time I am commuting or deadheading (yes, there is a difference) in uniform, I ALWAYS board in zone SKY unless I am extremely lucky to score a seat in the F cabin, in which I board in zone PREM. I never "pre-board." Yes, when I'm in 40F on a 757 my boarding pass shows Zone 2 or Zone 3, but I always board in SKY and have never had pushback from a GA. It is a rightfully known courtesy to allow crew members space to stow their bags. I never stow mine in a row that isn't in the same cabin as myself. Our crew bags are incredibly important and there just simply isn't enough time to check them.
I have heard of some airlines requesting jumpseating pilots to pre-board to complete a credentials check with the Captain, but have not experienced that myself.
Also, crew members should not "skip" others in line, unless they are working on that specific flight and have duties to attend to. I have done that before, but always politely. Usually when people see me rolling my bag down the jet way they naturally allow me to pass.
Traveling across the country tomorrow night as a revenue pax. Going to be strange boarding in Zone 1 (I have the DL AMEX). But at least I can enjoy a drink since I'll be out of uniform!