The difference between the level setting for the mains and the setting for the sub reflects the fact that they have different sensitivities. Obviously the sub delivers a higher volume for the same input than do the mains. That's not surprising since small monitors tend to be inefficient, but part of it is also the fact that the sub has it's own amp and the gain setting for that amp circuit is going to be different to the gain setting for the 2807's amp. There's also a difference between the levels for my mains and for my sub. It isn't as big as the difference in your settings but then I'm using floorstanders and a REL sub, so you would expect to see differences in our settings.
I don't know how your NHTs perform but, given your room description, I'd say things would tend to sound a little, perhaps even a lot, bright without EQ. I suspect that what the EQ is doing is a boost at the lower frequencies handled by the NHTs in order to try and match them to the sub. There's probably some roll off too at higher frequencies but the EQ chart doesn't give you a real good idea of what is going on in the top octave.
In my system, the AutoEQ result using the Audyssey curve sounds extremely good. I also have a hard room, ceramic floor tiles with no covering, large windows and glass doors to the patio. a glass display case full of ceramics, and an aquarium. Things sound bright and hard without the EQ but surprisingly well balanced with it in my room.
One thing I did find, however, was that I had to remove the footstools in front of the couch when I made the measurements. I got phase errors on at least one speaker every time I tried the initial test with the footstools in place. I remove the footstools, close the windows and any doors opening into the open plan area that are normally closed, plus I also close the door to the patio which is often open. With no obstructions on the floor between the speakers and the microphone, apart from the couch I sit on which is too large to shift, I get very good results each time, and I've repeated the setup several times now due to changing my front speakers and then adding surrounds when I went from 2 to 4 channels, and also when I shifted the couch forward by a bit over a foot to reduce the viewing distance.
David Aiken