Well, your problem is essentially an aesthetic one, as you are uncomfortable with the complications of adding additional cost to certain Advantages when specific circumstances arise. I can certainly empathize, but I would tend to place less importance on finding an immediate solution.
So the question is, how to simplify the matter? We could separate those, "dangerous," Advantages, but then we are essentially increasing their cost when
any other Advantages are included (for example: Variable Advantege, Based on ECV, AP, Adjustment Powers that work on multiple Powers--at once or not--Does Body, Increased Range, No Range Penalty, etc.). Are you sure this is what we want? Will we need to re-adjust costs for your proposal too?
Maybe we should just make a flat increase to the cost of these dangerous Advantages right off the bat; give them the worst case cost, or some middle cost based on how likely they are to be combined as we fear. You can't argue that
that won't be simple.

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