The current center of mass should be the rotation point for any ship; if it's not (and I haven't explicitly tested this recently), then that's a physics bug that needs fixing.
This does not appear to be the case when respawning old prints, i have moved stuff to the back but cant get the axis to move. Also, the show center of mass option doesnt work.
Have you tried creating a new blueprint from the old spawned-in ship and then spawning that one in? Once you've toggled the option on, you have to sit in a ship before its center of mass will display or update.
Yes, ive spawned new and it always turns from cockpit, and with multiple cockpits the axis will move depending on which one you sit in. i have a video to show this, ill try and remember to post it later.