They've both said they thought the rule itself was crap, with RTD saying that if it was up to him he'd ignore it or handwave it, but said by then it'd be somebody else's problem. RTD's tabled theory was simple: the limit wasn't a genetic/natural thing, but an artificial one imposed by the Time Lords, like a speed limit (probably ingrained into the Eye of Harmony) to prevent immortality, because immortality led to corruption. When he was running the show he suggested that either a) with no Time Lords left there'd be nobody to police the 'speed limit' or b) In the later days of the war they removed the limit entirely to ensure they had as many soldiers as possible, and they're no longer around to reinstate it.
Moffat was always somebody who maintained you had to fix it on screen because it was so ingrained in the public consciousness in Britain. It's a weird thing, but I was born the year the show went off air and prior to 2005 there were certain things I knew - I knew what the TARDIS was and looked like, I knew that the Doctor was a Time Lord, I knew what a Dalek was and that they shouted Exterminate, and I knew that the Doctor had 13 lives. It's weird how that concept, only mentioned twice I think on screen, took on a life of its own.
It comes back to that quote I posted a page ago where I compared the two, where RTD said for the sake of a good story he'd trample over or rewrite almost any piece of old Doctor Who lore if it'd make the show good and help him tell the story he wanted, while Moffat described himself as being "clinically unable" (or something like that) to contradict old Who lore because he's too much of a stickler for it.
