Dan

You could do with getting the lower area higher by using plywood and then tile the whole thing. I think. What sort of height difference are we talking about? A few mm? Materials-wise, it's a case of BAL Fastflex on the floorboards providing they are screwed or fixed really well, and two part flex on the plywood, at the most. Or the whole lot with fastflex and if it's just a few mm difference then you could swallow the difference with the adhesive.

If I read your post right, that is.