It would seem to me the auto' would be more pricey too. I think the AFM in the L99 would have something to do with that since it sounds more complex than the LS3, valvetrain-wise. I'm sure it'll be underrated and under tuned. I'm sure getting rid of the TM would help a lot. I can tell you the difference in my car with the TM on and with it off were litterally night and day.
05 Hummer H2 SUV on OEM Air Ride
Forged 11.4:1 408 LQ4 (K1 crank & rods; Mahle pistons)/CPP LS3 CNC heads/BTR Stage IV LS3 cam/home ported L92 intake manifold/ported 90mm TB/custom Volant CAI/mid-length headers/AFE dual 3" CB/Corvette Servo/el cheapo lift/Cognito UCAs/Sphon poly adjustable TA/Sphon adjustable rear LCAs/e'fan conversion/DirtyMax radiator/Moroso catchcan/HPTuners/HID conversion/LED exterior lighting/LED interior accents/Autometer Cobalts/AEM WBPioneer AVH-5600BHS/Pioneer GM-9601/2-Pioneer TS-W310D4s/Obcon Labyrinth dual-12 box/lots of other little stuff