The Oldest Question in A Fake Universe - not "Who Left The Gas On?" After all...

But Doctor, Who?

Think about what you've seen. Season 5's The Pandorica Opens/The Big Bang.

Reality was destroyed by the Tardis explosion - the Doctor flying the Pandorica into the exploding Tardis was able to reboot the Big Bang, thus bring back the Universe. The price however being the Doctor, trapped in the nether regions between worlds and never having been born as far as reality is concerned.

This Universe, basically, isn't anywhere near as old as you'd think. 

In this reality Amy had to remember the Doctor into existence - that isn't the same reality as the one everyone started in.

And Doctor Who? gets to be the operative point simply because Amy had to remember him into existence.

It's all been just a big fat lie!

We assume that nothing changed after The Big Bang - Steven Moffat certainly doesn't appear to do very much to dissuade us from the impression. 

But step back and look at logically - a person can only possibly remember what they know, and the very furthest back Amy's formative memory's of the Doctor go is the Raggedy Doctor she first met as a child - the Timelord not yet settled into his new incarnation. 

Not quite yet fully 11, not quite yet entirely stopped being 10.

At the time Amelia first met the Raggedy Man she remembered into existence at her wedding years later, technically he was still partially two incarnations.

There is no further back than that as far as this reality is concerned.

Reality was made to be this way for this exact reason.

If in doubt. Always go back to The Library.

Creating a version of the Doctor, stripped of his actual life - it's essentially no different in concept than the digital version of Donna saved to the virtual world of The Library's mainframe, her actual physical self elsewhere externally.

In the form the Doctors in, just like Donna, his history can be altered, his life integrated into a completely different history. One that never was, but what the Doctor believes is true.

Just as it was for Donna. The difference is simply in terms of scale.