They are still separate at the moment, but that is a good point. Unless there are situation where a player might not want a ship flagged as a tanker (which I can't think of right now), I should probably remove the checkbox and just assign the tanker flag automatically.
I'd suggest (since it sounds like the checkbox etc are already in place) you should just leave it there and allow players to toggle it, but if someone adds a refueling system to a ship, turn it on automatically, and if someone takes all those systems off, toggle it off automatically.
If, as I suppose, the checkbox is already built and linked up as before, this seems both easier and a good way to avoid accidentally removing edge use cases. (Maybe, for example, someone wants to build a tanker that is huge and carries a lot of fuel itself, but relies on a small swarm of 'fuel movers' that themselves have 2 sets of refueling gear - one to connect to Big Momma, one to connect to the dry ship. I dunno.)
You can then sweep through and remove it later if it turns out nobody's using it.