Although a separate EQ for the tuner would be fun, it's not the right tool to solve your problems.
First, the extra bass in the tuner is a specific "bass-boost on tuner" feature that they added. I think most everyone on the BBS would like to see that one be user-configurable. (On my system, I think the bass boost works perfectly on AM bands but should be disabled on FM bands.)
The relative volume offset of the AM and FM bands should (I think) be configurable. I, too, get volume offset problems when switching between AM, FM, and MP3.