If you skip the tier 9 upgrade by getting the tier 10 upgrade by using the super reward bag at the end of the main questline, Penguin Bay still sells the license for the tier 9 upgrade that was skipped. This can be fixed by adding "shipupgrade7" to the exclusiveQuests array in the patch file (semi-permanent fix, only permanent if the thing underneath is not possible).

If there was a way for a merchant to sell an item if the player completed a certain quest, it would be doable to have the Penguin Bay sell a fake version if the ship was already tier 9 and the main questline completed. I don't know if this is possible.