Do you think it will even make a difference? Only thing I can think of is it wont have to do all that processing of the bose amps eq'ing.
This is andy's standard answer to the question, it seems to be a pick your poison option. Neither way is bad though....There are advantages to both. If you use line level input, then you probably have a stereo 2-channel signal, so MS-8 doesn't have to reconstruct one. The advantage to high-level input is that no ground loop is possible (no chance of engine noise) because it's isolated from ground by 6V.