The problem you would find there, I think, is that it is the support ship which docks with it's target, not vice-versa.
This would lead to two problems that I can think of....
1) A small cruiser trundling it's way halfway across the battlefield to re-arm you, very easy target. This can obviously be improved by you flying toward
it2) Freighter Judo, where the freighter spins round at ridiculous angles and speeds in order to line up with you, quite often cracking your wingmates one in the process. This is almost as funny as Freighter Baseball, where a Poseidon or the like weilds something 15 times it's size with deadly ferocity

That said, I don't think it would cause a problem to set a ship with Freighter and Support Ship flags at the same time, best bet is to give a go and see what happens
