Seperate ships clamped together by robotic parts should be treat as one ship by the use of “sticky pads” that attach like grip pads and are released by EVA by engineers, allowing robotic clamps like the claw, but to fit around ships if the claw cannot be put in the right place, like for example requiring an engine or heatshield to be added exactly to the top of a ship for a rescue, but it has a solar panel sticking out on a piston meaning a klaw wont work. You can design robotic atrachments ato clamp the whole ship, but when warping they drift apart as they are seperate ships, so the sticky pads would clamp on and behave like the claw to make it into one ship possibly with the fuel transfer disabled as that would be silly, bu allowing warp and allowing transfer of kerbals.