Hm, sounds interesting. Had a similar issue on a remix of a piece of classical music
IMHO, although you can have the tempo of the project follow the stems, it really doesn't seem to help. The major problem is if you drop in loops, the loops will not still be right (or not sound correct).
So, I believe it's better to quantize the whole thing to a locked-on 4/4 beat.
What I usually do is take the whole mix, determine an approximate tempo (by using Tap Tempo), then turn audiosnap on and have it do a first attempt at transient detection. I then remove all the ones that are not on the 1st beat of a measure. If it's missing them, then I add them manually. You may not have to do that for the whole song, but if timing drifts much, you will probably want to do that.
Then I manually move the transients so they lock on first beat of a measure. If you have the other stems loaded, their transients can be moved as well. I then turn on the metronome and see if everything seems to be locked up. You will also want to use Radius Mix for offline processing and freeze the track every now and then to check the quality. You also might have to try another offline processing algorithm if it seems to sound better.
It's a bit time consuming, but what I've found is that most remixes will use only a few parts and even those parts get repeated.
I'd try it now, but I'm visiting my folks for the holidays, and a long way away from my DAW. :-)
It is true this is much easier in Ableton. It's one feature that I would like to see improved in Sonar, along with easier chopping and sampling. This would make Sonar more idea for remixing.