Not sure if this is the right place to report bugs, but I encountered some with the Tylos Exo-ship. It seems like the second form doesn't receive some bonuses/maluses.
The 2nd fitting doesn't receive the bonuses from fleet skills. I'm not sure if this is only with Second-in-command, but it's easy to test. An unpiloted Tylos with any speed increase officer and the second form will be slower (not just in the fitting tool, but in combat as well).
It does receive the bonus from the pilot skills like Helmsmanship (though this doesn't show on the fitting, only in combat).
The second form also shows 100% combat readiness (in combat), but doesn't actually receive the bonuses from it. A Tylos with no captain, no officers at 50% CR will have the same stats in both forms, but any other percentage and they're different. The second form also doesn't malfunction even if you start the battle with 1% CR.
EDIT: Amazing mod by the way, already lost close to a week to this one and second-in-command. Thank you for the amazing work!