Well it isn't like RTD and Moffat don't talk to each other. I'm pretty sure RTD would have, at the very least, run by Moffat anything he wanted to write in SJA and even though he isn't show runner I'd imagine Moffat would have some level of veto over what goes into SJA?
No. Moffat is showrunner of Doctor Who, not supreme overlord of the Doctor Who franchise. SJA is RTD's show, he can do whatever the hell he wants with it and Moffat can't do a damn thing about it.
I'm sure RTD and Moffat do discuss things, and sometimes Moffat may even provide his input and RTD might even takes his advice. But in the end, RTD has the final say when it comes to SJA.