I'm not sure why there is such a difference in settings between the two units. I didn't see it in the 990 manual just now, but the 950 manual recommended calibrating to 75dB (which is what I did). I did the same with the 990 prior to running the auto-setup, and the auto-setup's values were very similar to my manual settings. I did not compare the settings on my 990 to those on my 950, but I don't think there was more than a few dB variation between the two.
Is it bad to set the trim above 0? I don't believe so. It is often recommended that you not set the trim control on an amp to close to its highest position, and I have run into trouble with an older Parasound amp hissing a bit when the trim was set high, but I don't think the trim settings in a receiver or processor are as susceptible to this as an amp. If you are concerned about it, find the highest trim setting (apparently +5) and shift all of the settings down by that value (so the highest trim used is 0dB) and see how it sounds compared to the way it was. You'll need to crank the volume up 5dB from where it was before, of course, but otherwise I would expect the change to have no effect on the sound.
Wow... Two 990's in Memphis already... That's sort of cool.