When we beat a stock map, it gives up the little medal at the bottom for the difficulty it was beat on. but that carries across the factions.
I guess this goes back to the whole relationship between the factions and maps/ship design. So along with separating the factions on the ship design screen, to separate challenges from each other. so if I beat the first mission using Federation, it wouldn’t also be completed for Alliance unless I beat the mission using the alliance.
i think this would give extra incentive to design ships for all the races, and I’ve found the missions are a great way to “beta test” each ship i design, seeing how well it holds up against each scenario or other race.
this could also be expanded slightly so that player vs. federation is included. the natural flow of the game so far directed me to use federation to beat the whole game and i was constantly tweaking my fed ships to get them just right. but now I have nothing designed for any other race 
since my fed fleet is sufficient.
to balance the amount of honor the player would gain from having to replay each map, the honor gained from a battle could be halved so it accrues at a slower rate. there’s one challenge posted in the mod forum that I have won with a fleet that used far less than the maximum funds so i got enough honor to buy everything in one go.