I have noticed in missions like mortain counter attack and carentan counterattack the starting troops are decided by the ones you completed the last mission with. is there a way to not let this happen/ are there any rules around those two missions in individual level runs since they are heavily dictated by their previous mission?

You can mine the entire top half of Carentan and it wouldn't change the RTA. Only thing I can think of that could be a game-changer would be to mine the Flak 88 spots in Mortain, or spam mines and MGs along the roads. Even then, Mortain itself is a timed mission, so you don't have unlimited time to prepare an optimal carry-over setup (this has pros and cons, but still worth noting).

But other games don't seem to be bothered by similar issues. SC2 WoL for one has an outgame resource system for the player to buy upgrades for in-game use, and they solved it by preparing saves for each mission with max possible resources.

Sure, unit comps and emplacement setups are infinitely more varied to produce savefiles for VS optimal resource values. But if it's replicable without cheating, I for one have no issue. And I imagine a meta will eventually emerge anyway.