The player should be paying for things related to their fleet, while the faction pays for colony improvements, patrol fleets, and wars.
Why this makes sense is because the faction should have a much greater earning power than the player's direct actions, and has a much greater financial footprint. The faction is hosting more fleets than the player after all.
How this can be balanced is by limiting how much money can go from the player faction to player by commission just like in normal factions, and having the faction finances actually reflect all fleet and colony upkeep accurately. Building fleets would cost money and all factions can decline just by running out of money.
Hopefully, this would make the game more interesting and punish poor colony building and planning by inhibiting the player from funding their faction through personal actions entirely.
This should also prevent some long-term power creep by punishing capital ship spam with prohibitive construction cost and upkeep over time.
