I would gladly pay extra real cash just to complete my collection. Having any piece of gameplay affecting content locked away to only people who preordered should be a practice that is considered illegal. I don't like preorder bonuses, but at least most companies that include gameplay related bonuses in their preorder marketing have the sense to allow people to purchase them at an additional charge. See the latest few installments of Mortal Kombat for examples alongside Tekken 7. All 3 of these games had a character that, does in fact affect gameplay, that you got for free with your preorder. They knew that to keep the field stable and competitive, they had to give late adopters a way to obtain those characters, even though it would cost extra. FDev could make some extra cash if they would just open the gates and allow people to complete their collection by buying the ability to have that "exclusive" ship. At this point, it's more a case of morals in my opinion. I hope they don't pull a stunt like this for the 2020 update, because if they do I won't recommend anyone purchase the game after the launch because they won't get the "complete" experience.
In all honesty, the commander deluxe edition should come with this ship instead of the skin packs currently present in that bundle.
TLDR: exclusive preorder bonuses should never affect gameplay in any way and should be cosmetic only unless they are sold later at additional cost.