There are always ways to excuse a poorly considered story arc and mystery. "The Doctor lies" is code for 'we're writers working to make a 60 years history hang together, so any mistakes in continuity are because of The Doctor being an unreliable source of information'.

Of course, you could be right, maybe Mrs Flood will have a great explanation that somehow tidies up a few issues here... but can't say I'm convinced that will be the case.

BTW, I saw an interesting observation that Mrs Flood is often wearing outfits previous companions wore... so that's curious.