All of these ideas, though interesting and well thought out, are way too complicated.
Functionality > aesthetics
Either way "undocking" needs a bit of work, because one wrong click or movement and you have an FPS dropping Physics disaster.
I like the idea of just having the fighters warp in and out of the ship when leaving and returning. Though it would be nice to see them flying in and out, it creates so much work for an aesthetic that is very insignificant.
Right now when you dock a ship or turret it just warps into place, there is no need for it to be any different.
As for using logic blocks and stuff...
No new blocks are really need. There just needs to be a way to group and assign things via the structure menus. So you can make fighter groups and such. Logic blocks could obviously used instead to undock groups.
To assign ships to a dock you manually dock the vessel then jump back into the core of the parent ship. In the structure menus there would have to be a "assign ship" under the docking tab so that the fighter is now permanently linked to that dock and nothing else can dock there.
When docking/undocking there would have to be a limitation of how many fighter dock at a time and how long before other fighter can dock. So "X number" of fighters dock then X seconds later the next "X number" of fighter dock. So there basically would need to be a que system. Can't have everything's docking and undocking at once, would cause worlds of lag.