If the balances aren't separated there is no feasible way you can ever hope to achieve balance in both modes. One MINOR change to combat parameters to one mode, has HUGE ramifications for the other modes. The overhead cost can't possibly be more expensive or more time consuming than having to make a new balance adjustment every single time a big patch comes out. It would be more cost effective, more practical, and more pragmatic to have these modes not be dependent on eachother at all. Separate the unit stats, equipment, perks, and Ai and focus on balancing those parameters specifically for captain mode, and once you achieve proper balance for that, you wouldnt have to constantly update the game to fix the problems you caused in skirmish because they wouldn't be wrapped up and tied into one update. Then you could make adjustments to skirmish combat parameters to make gameplay more enjoyable for them without affecting the balance changes you made to captain.
Edit: I'm probably coming off as frustrated, but this is only because the most important games of our Captain League season were essentially ruined because of 1.5 and we captain mode players really do feel like an adopted step child that is unwanted sometimes, especially when we read the forums and most of the discussion and balance changes are focused primarily on skirmish with little thought given to us. We don't exactly feel like a priority, and that's sad considering what an amazing and active captain mode community you have for bannerlord.