Hello,
I am actually working on totally re-vamping the squad/unit deployment system and circuit control, to allow more flexibility and it would support what you are talking about better
the targetting behaviour of the droids should be normally "Distract by anything" which should include seeing and stopping and destroying non-military buildings from enemy forces, but the biter AI doesn't appear very good at it, and the bots use biter AI. It has nothing to do with pollution, in this case, just the distraction type and the type of buildings nearby (in the hidden game code, I can't control this part)
the colour on the map is based on the unit's prototype and is fixed, and is the same for all bots in the game regardless of team. It's not a run-time adjustable value, as far as I can tell. I'll ask a dev on discord about this.