I'm convinced the best idea is, like others seem to agree with, to treat each armies references to "friendly" models and such seperate. Much like your rules wouldn't affect the enemy units, although you don't shoot your allies.
That said, there ARE rules which could be used, or exploited even, between allies. Rules that affect all models, say within x inches from the soure. The KFF is one. I'm fairly sure Fateweavers ability to make every invulsave within his aura rerollable would work too.
But like I said earlier, the actual game is for intent and purpose written for 1v1 games, so references to friendly models would be your own. Any actual teambattles need houserules, and the easiest here is to treat each army seperatly.
