The stronghold auto formation for the ship missions do not properly use the best available pirates and ships to get the better bonuses and here are some screenshots with the auto formation and the manual setup done by me as player to show the difference.
It seems that the rare and epic pirates that have double bonuses are not being considered properly.
Kinda sad that there is no comment at all from admins/devs after almost a month on this. If they cant fix this they should at least remove sailors from being limited to one boat if their auto formation code is not going to take that into consideration.
Is there an update on this? I can confirm this bug exists as well. Often you have to manually select a ship in order to pick a crew that matches the bonus trait. The auto select feature starts with the wrong ship ignoring a potential better crew that is exclusive to another ship.
I was about to comment this same thing but realized you replied to your own post so all is sorted. Yeah the game auto form bases on the ship resistance. I often have to manually pick the ship and crew myself because of this. Not that adaptation means much but I do it for the achievement.