e46 M3 with coilovers is a very capable track car.
Last fall at a Road America event there were two of them, one a vert. On the straights I'd close on them no problem -- almost to the point where I'd have to lay off the gas -- and then we'd come to a turn and shortly thereafter, well, they'd disappear...
Now I know my e39 can't compete with the M6 on track in any way. However, I attended the event with a buddy in an R8 V10, and while he's no professional driver, he waved them by on more than one occasion as well. And most of the time when they passed me they were running with a seemingly skilled driver in a Heffner R8, so...
I agree with Hasan in that this isn't that apt a comparison -- the M6 is a true GT, but to address the question posed --
Based upon my experience I don't think a stock M6 hangs with a modded (suspension) e46 on anything resembling a tight/technical track. M6 "destroys" it only at a drag strip.
Based upon your tone, I presume you may be posing this question following a (friendly) exchange with an owner of an e46 with suspension mods. I would advise that you not get too cocky with him... you may be in for a surprise.