The pitch wheel will bend all notes playing on the channel, so not good for poly.
MIDI itself does not define microtuning, but synths are free to assign arbitrary pitches to midi note numbers.
If you want poly, the thing is to find a synth that supports microtuning, alternate scales, etc, then use scook's technique to keep track of what notes the MIDI note numbers refer to.
Cakewalk's dimension pro, rapture and z3ta+2 are said to support alternate scales ("scala" (.scl)
microtuning definition files).