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He sets the bar nowhere, which is why we're pleasantly (and sadly) surprised when someone actually does say "whoa, wait a minute." It is unclear why Comey waited as long as he did, but I give him credit for for his actions in 2004. He was confirmed as Deputy in December 2003, and the showdown occurred in March 2004, so it's possible he cried BS the first chance he got to really review the program (the first time would have been ~Jan 25 if they were on 45 day review cycles, so it's hard to say if Comey would have reviewed it then).
Clearly Comey sees a line to be drawn, and he draws it more to the right than the average Saloneer, but that's not really surprising for a political appointee from a Republican president. I wouldn't expect him to be a liberal/progressive. That said, it's clear that the White House has drummed out anyone in the Justice Department who thinks a line needs to be drawn anywhere. In the cage match between John Yoo and the Constitution, Yoo has clearly won hands down with the Bush Administration