Clarification:
You don't have to have a pirate AI or player in a mission to affect the cartel layer, or for cartel political tensions to mess up the DV results of empire vs. empire missions.
Again, these should be retested, but my experiences:
If all cartels are friendly to all empires, one of the situations I described above happens. Essentially, no matter which empire wins the battle, the serverkit gets confused about how to apply the win/loss to the DV. The possibilities are strange. There may be no DV change for the empires, or their results can hurt the cartel DV underneath. What tends to happen is either nothing changes, or the changes also hurt the health of the cartel DV. Once that cartel ownership flips to neutral, the players begin to hurt their own hex.
In RT3, we had an allied cartel grabbing hexes underneath their enemies and allies to affect the empire DVs. If they took the cartel layer of an enemy hex, or flipped a hex neutral, the home empire couldn't boost their DV, and could possibly hurt it. If they took a hex that was also owned by their allied empires, then the defense missions there WOULD raise DV. The trouble with freeflying pirates grabbing hexes is the players can't monitor cartel layer DV, and can't fight off the invading pirates. They also can't tell how their cartel players' missions are affecting things until a hex flips.
In SG(can't remember the number), players could fly both empire and allied cartel, but not only was it hard to keep track of things, but generally people didn't want to play as a cartel. Even if you can get the 2-layer assault/defense coordinated and have all players conscious of both, you still need players to put in roughly equal time as cartel pilots as they are putting in as empire pilots. Oh, and of course there are bugs even when you seem to get this all straight.
It's such a twisted mess, it's hard to get solid data on what happens when certain conditions occur. Our best bet at this point is to find a way for the servers to ignore the cartel layer when determining empire DV changes. If we could do that, we'd be a giant step ahead of where we are now.
At this point, I really don't know what else to try besides putting up variations of .gf settings ad nauseum and testing the results.