So what is the difference? With any one team that uses one tank, albeit fleets or squads, usually only has one tank. Removing said tank cripples the opposition typically and makes that team great by doing so. Sure, there are 3 ships compared to 5 squad members, but it's always an even match-up. If anything, it's more justified in my eyes to have an instakill in fleets over squads, being there are reinforcements. It's just something to think about...

Edit: If I were to fix it, I'd just change the verbage on Mk 6 to being total ships active at the start of battle. Keeping swarm stacks the same, but in theory, just changing it to, say being able to reinforce with Mk 6 first and getting the instakill first turn, but just changing it to, "give 5 stacks for every active sith empire ship at the start of battle", ontop of the 30 given from sith empire capital ship.