are originally team colored? For example, the flag on the Blademaster's back is really annoying, but I can't alpha it out, or it just turns to a solid team color.
Is there anyway to take out the teamcolor short of modifying the model?
No. It is teamcolored there because of a model setting for that geoset. However to remove it is not all that hard even if you have no idea how to model. Just open the MDX as an MDL and change a few lines of text and your done.