Great stuff there - much appreciated!
After having a closer look with the team at your screenshots and files sent regarding Captain Ibrahim and his perks during combat, I can indeed confirm that the current mechanic does work as intended.
See, the confusion might come from due to lower HP once you leave/conclude the combat, as the 20% HP bonus is also being taken away right after. Essentially, the bonuses Ibrahim offers are similar to 'bullet sponge' mechanic, where whilst in combat, his ship is able to soak up more damage than what the base stats offer. Hopefully this makes sense.
If you happen to have any further queries on this, get back to us and we will be happy to look into it for you!