Trim levels are just relative numbers. There is nothing wrong (or different) about negative trims. The point of calibrating levels is to (1) achieve the same level for every speaker and (2) play at film reference when the master volume is at 0.
If the speakers have high sensitivity, or are close to the listening position (or both) then the trim levels will show up negative to achieve the goals mentioned above. It's not a good idea to change the trims because that will throw off the Dynamic EQ calibration. If you want the system to play louder just turn up the master volume.
SPL meters need calibration so it's possible that there is enough discrepancy between the meter and the Audyssey mic to show different readings. Also, the internal test noise of the AVR is a slightly different way of calculating level than what Audyssey does using psychoacoustic weighting of the measured response.
In any case, it's not a huge deal to change the trims if you feel the need to (keeping in mind the implications on Dynamic EQ). The most important part of Audyssey--the filters--are not affected by trim levels.