You probably *do* want to adjust the supply use or CR deployment cost. Conceptually, I think that's what you're looking for.
Not quite. I'll explain why. The base logistics of the game is 20. The skill line you choose for your "primary" in my mod determines your game-play choice. Combat allows you to use roughly one ship (but a very powerful one) and an assortment of fighters (modified for a different role in my mod), but due to the varying deployment costs of differing hullsizes, or more importantly their logistics cost (not in supplies per day but on the logistics score itself), prevents this from being applicable since you could say, field 4 frigates at 5 deployment points/logistics or a single battlecruiser for 20.
The way it works is for your primary skill line to start at 10. The bonus for combat level 10 homogenizes the logistics cost of your flagship only(on your logistics score out of 20) to always equal 12.. leaving you 8 points no matter what ship or hull-size you pick for support ships or fighters.
Leadership on the other hand, reduces the base credits cost of all ships by 50% (ships cost way more in my mod) and gives you a large percentage of logistics (40 instead of 20) upfront to account for fleet style play. So for this skill choice varying deployment costs is essential. It was just easier to modify the flagship cost in combat rather than modify "all" ships costs under leadership
The point is to make skill choice determined on the a new game start to be very impactful on the playstyle with the option to hybridize slightly starting at level 20 with the addition of 5 more attribute points.
I could go into the reasons for this choice but it wouldn't be relevant to the thread and would take too long haha. I know this is not how vanilla was envisioned, but I am experimenting with an rpg style skill system that specializes a bit more strictly.
Allowing only the flagships deployment/logistic score cost to be modified would not impact performance at all since it at the most would be the addition of a single ship. Balance would of course be implemented in other ways through the skill system.