Not really sure what you are getting at, but the MOST important factor about Zeus/CoA/CDM is the defense boost. There is NO other way to get this boost other than leveling zeus/coa/cdm.
So going back to "but do the boosts from Zeus/CoA/CDM affect terrain and unit boosts?"
Well, yeah in a round about way, if your defense boost is reallllly high, it will take longer time for the opponent to kill your unit.
So we can deduce that a lower defense unit will die faster in unfavorable terrain when compared to a higher defense unit.