One variant of this design you could try Klondike307 would be to divide the through-deck into two landing areas. Then split the front landing area into two decks, one for shuttles, one for workbees, each area with its own doors. Then add a bunch of airlocks along the hangar base. And a few extra tractor beam emitters.
Now you have a repair ship that can warp in to assist a disabled ship (maybe carrying a collapsible drydock in the aft landing area for the duration of such a rescue mission.) This variant could also act as a tender for shuttlecraft and small scouts in locations where spacedock or starbase services weren't practicle.
----------------------
The only real complaint I have about the design as is are the oversized windows.
Very interesting concept