you are correct, the '01 and up Corvettes are making around 10 rwhp more than the pre-'01 cars. This is due to the LS6 intake and slightly different cam specs. But, the '01+ F-bodies also got the same LS6 intake installed. They also dyno about 10 rwhp more than the earlier LS1 F-bodies.
The larger MAF as found in the Z06 is not making any gains, it was really just a slick way of incorporating the IAT sensor into the MAF housing and making a cleaner harness. When properly tuned, the larger diameter MAF shows no additional gains over the standard LS1 MAF size. Its larger cross-section might help support HUGE power setups though, maybe 600+ rwhp cars.
C5's do have a little more drivetrain loss than f-body's. The c5 has a rear mounted tranny directly to the differential, uses a torque tunnel and half shafts, and has larger heavier tires. The f-body has a solid rear end with a drive shaft.
The f-body and c5 dyno results I've seen are always very close year to year.
I've been trying to do a little research and found that the part #'s for the cam, throttle body, and intake manifold are different for the F & Y body LS1's. Don't know what the differences are, but could this account for at least some the the HP difference?
2000 TR FRC
WSIR 2.5mi 1:40.48
The camshafts in the Corvettes were always a bit different than the F-body camshafts, but not any more aggressive. They were designed to make up for the lack of EGR system on the Corvettes. The F-body had an EGR system (just emissions crap) between 98-00, before the LS6 intake was installed. Now, none of the LS1/LS6 cars have the EGR (Exhaust Gas Recirculation) system.
The throttle body part numbers were different because the C5 uses "throttle by wire" and uses a servo motor in the t-body to open/close the blade. Its fully electronic! The F-body uses the simple cable-driven old school setup. Other than that, the t-bodies are the same size and shape.
Intake part numbers were different due to the EGR stuff I mentioned above. F-bodies had a hole behind the t-body for the EGR head, Corvettes had no hole there. Other than that, the runners and internal volumes were the same on both cars.
The motors are almost identical, which is why Corvette guys would really benefit from our LS1/LS6 Engine section discussions involving internal motor work and camshaft selections, etc...