they're not really meant to balance... They're meant to moderate progression, as you said. The issue is that once the player stabilizes it becomes possible for them to endlessly grow in the amounts of money. Roam about with a gigantic fleet, have a bunch of colonies and just print it.
Why is this a problem though? Every RPG with persistent progress eventually reaches this point. Besides, even if crew costs were raised by some absurdly high % couldn't theoretical end game player just plop down some more colonies to cover the costs? How expensive the crew needs to get until it provides logistical challenge to end-game player, considering every bit of it will be at the expense of early to mid game progression, probably making it an unbearable grind.
