By “carry” I guess you mean one will get stronger than the other in average, so after a few dozen hours he will kill stuff faster and improve this partner’s loot rate.
If that’s the case, you are depicting an always perfectly balanced situation. ^^ Because you didn’t take into account that the weaker player will also drag down his partner. So while the one playing in the weak mod would get more loot than a solo player in same mod, thus reducing the imbalance, the player in strong mod will get less, balancing it out too.
I hope that makes sense. ^^
Anyway, that would never happen in the competitive environment we’re talking about : if one mod is known to be the best, both players will play the same anyway, no matter what they prefer to do.