Hey, just an idea for your great concept from someone who has no idea what ksp's modding framework looks like.
Instead of forcing players to start with their tanks empty, which will cause the problems you listed (dV, CoM), only allow them to fill the tanks with the amount of fuel their base has. Essentially, create a base resource that lists the current amount of on-hand fuel. That way, they still have to create all that infrastructure, but they don't have to fuel in on the pad (unless you want that of course).