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Even if the tabletop maps are very limited in scale, actual campaigns are large enough that most HQ's wouldn't even see each other across the battlefield. They'd likely be engaged in different missions across a planet or even a sector.

For a proper Apoc game, there are no rules saying they don't work together, so don't sweat it. Otherwise, demand that Dark Angles and Space Wolf HQs also do a duel before the match, or that Black Templars charge allied psyker/xeno units and so on.