Thanks for all the replies so far.
I initially suspected warped rotors, but hell, it's still under warranty - why get dirty?
I had a Ford Escort, so I've got plenty of experience diagnosing warped rotors and seized caliper sliders. The situation with the Scoob is somewhat different, in that:
1) If it's warped rotors, then I should notice pulsation/vibration whenever I use the brakes. In this case, however, hard braking yields no vibration, while light and moderate braking causes vibration.
2) Why would the rear brake pads be worn to the same degree (50%) as the front pads (assuming the dealer is accurate/honest in the wear estimate)? From what I understand, the fronts account for 70-80% of the stopping power. If anything, the fronts should have crapped out before the rears (which were just turned for excessive runout), unless the stock braking system is "perfectly" balanced wrt pad wear?
3) The fact that pulsation/vibration is only present during light/moderate braking leads me to suspect a possible problem with the tandem brake booster. As noted above and in tunered's reply, I would expect warpage to cause vibration whenever brakes are applied. Could the "dual-stage" nature of the vibration possibly be attributed to a malfunction of "wimp" stage (low boost) of the booster? I've lurked for a while and have read the threads regarding poor pad life (i.e. "You drive like a maniac"), but have not seen any description of the particular behavior I've noticed.
As far as PROPER repairs go - once the brakes are out of warranty and it's my dime, I'll definitely replace pads and rotors all around, add SS lines, clean & lube calipers, slides, and bushings, and do the StopTech bedding procedure .
Until then, I'd like to have as persuasive an argument as possible to convince the dealer to fix this problem on THEIR dime.
Please keep the suggestions coming - I'm very grateful.