I've changed the boarding scripts so that ships without player docks (Xenon K destroyers seem to be the only ones currently...) have things done a little differently.
Instead of needing to dock and put your crew members in there manually, you automatically get a full set of crew members (Captain, Defense Officer and Engineer) already on board to run the thing.
How do we retrieve the Marine Officer without a dock? Well, the marines all come back aboard on their pods automatically (and instantly!) after capturing the ship. The Marine Officer should be able to do the same.
Since the only reason any ship wouldn't have an access hatch would be if it has no living pilot, a.k.a. run by A.I., think of it as "we gave the Marine Officer an AI/AGI hacking/remote control module slaved to the Skunk that they can slap onto the main systems after capturing the ship" or something like that.
(So, after capturing, the module we placed there would take orders from us, just like Captains would do, defend/attack and repair itself just like Defense Officers and Engineers do. That's what the "free crew" I put there try to simulate. ...The humans you see on the comms? Um...they're holographic avatars!)