I guess my solution would be keeping the "modes of play" separated somewhat.
Meaning, that each side has X amount of points for
BFG, AI and
40K, and has to field at least XX amount of troop transit ability. This could be a way of fleshing out the campaign.
Example:
40K mission, Extraction.
Your force has been outmaneuvred by the enemy, and you need to extract them from a hot zone. Target for defender: Hold on to a mission objective (airstrip or something) for x amount of turns.
This would then open up for a AI fight, where you need to bring a set amount of troop carriers in and out within a limited number of turns. And of course your enemy wants to destroy your transports.
Just some thoughts, hope it helps