Hmm. That stinks. I was looking at getting a Skinomi skin and the screen protector. The one they had for the Prime actually had it cut out where the dock overlapped the screen so that the screen protector wouldn't interfere with the dock and get all bunched up. I assume the ones for the TF700 don't have that?
Equal Opportunity Hater
HTC Droid Incredible - Rooted - Running In-Sensitive Minimalist
ASUS Transformer Infinity TF700 - Rooted, Unlocked, Running CleanROM 2.0
Samsung Galaxy Nexus - Rooted - Running AOKP JB