This sounds like Moffat wants to do something with the idea that these characters are connected. I can't think of anything more inward looking than explaining why the Doctor looks like a one-shot guest star from five years ago and a star of a spin-off series from four years ago.
It's the same kind of incestuous bullshit that heralded the end of televised Star Trek; once you've got entire storylines dedicated to explaining away quirks of production, you're out of ideas.
I got my hopes up when I heard this originated with RTD. I got my hopes dashed once I read what it actually was.