Hi!
Today I ran into this funny little bug which basically allows you to "clone" your player character with all it's skills and thus have all ship in your fleet benefit from your skills. I thought replication method is easier as shown than explained so here is the video I made about it:
https://www.youtube.com/watch?v=eaNpWexFHjcAfter replicating the steps in the video, one can undock and use his ships like that perfectly fine.
Also worth noting that if you try undocking while having your commander put in storage hangar along a ship your commander seem to be automatically back in the first ship on your list of ships.