how to make a docking clamp
Step one create a ship that IS a dock for your supermassive ship, make it as small and compact as possable with the core in the exact center.
step two is to create a dock on your station for the docking clamp. then simply dock your adapter to the station, then your ship to the adapter.
this alows you to bypass the station based docking port and intersect it with blocks creating the oportunity to create 0 clearance docking and things like airlock walkways that would normally intersect into a docking area, just make sure it doesnt intercsect the docking area of the adapter.
using this you can clip into the ships docking area as much as you want.
dockception.
this works best with large ships and ships with odd core placements (as this lets you adjust the docking port on the adapter to an off center position to center your ship in the area you want)
You do not need to include room for the docking area of the adapter in the station dock as it doesnt count towards the area the adapter takes up, only the actual blocks take up space, so build a simple core+dock+enhancer adapter to be as compact as you can and you win!