I do think a lot of people think RTD has gone in and told Moff he is using 11 and sorting out the regens, whether he likes it or not. Like he stamped down his big size 12s and moff could do nothing about it. SJA might be Russells baby, but everything relating to current Doctor Who will have to have been signed off my Moff first. RTD can talk about regens if he likes without Moffs permission, but if that was the case, Moff could easily pull 11 out of the mix and write something in the main show that glosses completely over anything said in SJA. Like Iceman said, this is an excuse for some to just take digs towards RTD.
The bottom Line is RTD can state whatever he likes, Moff can either follow or contradict, and a few years down the line whoever takes over from Moff can do whatever they like - it's just something where you have to go with the flow.
For me the best solution would be for the Doctor to state that they were originally limited to 12 regens but Rassilon removed this restriction during the time war.
