I tested it before posting. The internal tanks need to have more free capacity than what you can put into the drop tanks for it to work. If the main tanks don't the refueling stops once the non-drop tank full level is reached. The fuel goes first into the drop tanks and after they are full the internal tanks get filled. I think if you remove fuel the drop tanks are also the first that get emptied, but not to sure about it. There was a thread about it a while ago with some technical explanations as to the why the tanks get filled with the refuel hatch open, something about pressure.
But I agree that this is a workaround and that it would be nice to be able to fill the drop tanks separate from the internal tanks in the rearm&refueling window.