The way I handle this issue is as follows: First, I make a list of all the ship mustering out benefits earned by the players. The first roll covers the down payment (20% of the ship's value) and each additional roll covers 25% of the ship's value. This is the ship's true value, not doubled for the typical mortgage calculation. These values also hold for pirates and their corsairs - they don't get the ship free-and-clear with one roll.
Second, I discuss with the entire group (ship rollers and those who don't have any ship benefits alike) which of the available ships, if any, they'd be interested in using. For example, one character might be a pirate with access to a 400 dton corsair, another was a merchant with a 200 dton free/far trader, and the final one (lucky party) is a belter with three rolls toward owning a 100 dton seeker. The party may not want the seeker (too small) or the corsair (too big, too many NPCs to run), so they might agree that their "credit" applies to the trader.
Now I apply the value of all the rolls toward that ship, and the value they "put in" is the number of full shares they own. Characters that didn't get any ships on their mustering out get tenth shares.
I don't have ship prices with me, so let's assume a seeker costs MCr 20, a free trader MCr 30, and a corsair MCr 60. The total "value" earned by the mustering out rolls is MCr 4 + 5 + 5 = 14 for the seeker, MCr 6 for the trader, and MCr 12 for the pirate. Full "value" is MCr 32, and one share is MCr 4 (least common denominator, rounded if necessary, from the down payments).
The belter used his uranium hits to buy into the party ship with 3.5 shares, the pirate has 3 shares, and the merchant has 1.5 shares. The other party members each have 0.1 shares (valued at kCr 400), and the total money available to buy/refit the ship is MCr 33.2. They can use this to buy a free trader free-and-clear with 3.2 million in upgrades (which won't go far) or a better outfitted one that they'll owe a small mortgage on.
Profits, if any, are divided among the group according to the shares.
Or they can use the 33.2 million as down payment on their "dream ship," and have to come up with 691,000 Cr payments every month. (33.2 * 5 = MCr 166 ship, mortgaged to MCr 332, 480 payments = MCr 0.691 per month.) They'd better get tradin'!!!