The captain skills of your ships in port affect the stats on team panels. The other modifiers such as upgrades are calculated correctly.
e.g. If your Salem in port has a concealment skill, it is nominally applied to the concealment of an enemy Salem, Even when the ship you are playing is Kleber.
If you need accurate ship stats, consider using my mod: TTaro Team Panel. It always displays the actual builds with the concealment skill taken into account.