It would be trivially easy for the show to handwave away the "twelve regenerations" thing. Indeed, they could simply ignore it and move on - the new series seems to be free to use anything from the old continuity it likes while simultaneously discarding anything it doesn't like.
But my question is this: why on Earth would they want to?
There's huge dramatic potential inherent in the Doctor nearing his last regeneration - amongst other things, he knows that at some point he's going to become the Valeyard, someone he really doesn't want to be. But there's other stories there - how does he face his impending death? What if, confronted with the horrors of the "lost incarnation", or the atrocities perpetrated by the Valeyard, or whatever, the 'last' Doctor decides he doesn't want to go on, and starts actively seeking his death? Conversely, what if that 'last' Doctor decides he does want to go on - what to lengths will he go to acquire a new regeneration cycle?
There's got to be a story there, and it's something they've never really done before (which, after 50 years, is saying something). IMO, they would be mad to just handwave it away or ignore it - far better to tell the story.
I'm not convinced there is dramatic potential - unless the viewer really did believe that the BBC was going to cancel the entire show. The viewer knows they won't do that, do there's no real tension. We know it's not the end.