I did go back and look at her door on iplayer. It doesn't match the Tardis and there is no reason why being blue is needed for a Tardis.
I do wonder though, as I mentioned above, if it somehow had Tardis "essence" to it - the first place we see a crack and the Tardis seems to end up there.

I ma leaning towards Amy being raised specially as part of a trap though, her whole set up as always seemed odd to me and the Aunt is almost to obviously suspicious. The whole series is about misdirection though...

I really do think Amelia is the person who grew into Amy - she might not notice her life makes no sense as she was the one living it, not looking at it from the outside. Plus I like the Duck Pond/ Amelia Pond thing

I'm leaning towards someone having been interfering with the Tardis all series, from when he first regenerated.