This is very confusing to explain - here's another try...
The 2Channel Offset makes perfect sense IF the sub offset applies to all surround modes. If you calibrate your sub, the calibration should apply to every surround mode on a digital input - Stereo and Upsample included. That way if you want to run your sub a little hot for all your surround modes, you can drop it for 2Ch up to -8dB.
But because the sub offset does not globally apply, you can't really use the 990 sub offset to calibrate your SPL's on your sub - especially if you're equalizing your sub. If I go balanced out from the sub output, through the DEQ2496 and to my SVS, I've got to have the sub offset at -15dB and the volume on the sub amps really close to zero.
Where this doesn't work for me is that if I leave the 2Ch offset at 0, my sub is now +15dB hotter on Stereo and Upsample than on PL II. Even if I drop the 2Ch offset to -8, my sub is STILL 7dB hotter for 2Ch music - and I want it to be LOWER.
So what this REALLY means is that the sub offset settings from -8dB to -15dB are completely useless and shouldn't even be an option because if I have to use any of those offsets to get my sub SPL correct, I can't get the 2Ch music SPL even EQUAL to the PL II SPL. If I have to select -8dB to -15dB sub offset, my sub SPL will always be higher than my PL II offset where I really want it 4-5dB LOWER.
This is really difficult to explain but it just seems like the sub offset not applying to the Stereo and Upsample modes is an oversight and should be fixed.