I made a new template. I do have several HV's and SV's docked but that never stopped repair before ( at least as far as I can remember) t2 repair block is ground lvl with nothing in the field that I can see
I'm pretty sure you have to remove all docked vessels from the vessel you are trying to repair first. Otherwise they count as an obstruction, at least they did in my tests. Otherwise you could end up with a situation where the docked vessels get buried by added blocks if you had them docked in a place with missing blocks. The game has no way to determine if they would be safe or not so they just count as an obstruction.