I posit that no one actually cares which mods affect which other mods, and all this is just bitching about something being made harder.
For example, TE's conduits entirely change BuildCraft's power distribution system (making it a lot easier to setup), and the OmniWrench changes IC's wrench system (all but removing it from the game - it's dirt cheap compared to any other option for what it does). Why aren't people in uproar about those? Oh, right. They make the game easier.
Sort of. I can agree the omniwrench has a cost to use that is a bit on cheap side.
But the Conduits they have a fairly more complex cost over BC pipes with the built in 5% cost and the need for mutliple machines to make them. VS BC pipes that can be crafted at the bench. It is a fair trade in my book.