Hi
Sounds like a good idea...the 1/2" is even better.

The wonderboard should be set in the thin set also(is this what you meant by bonding?)..it will fill any void you have under the board, and give you a nice solid surface. Thin set again of course for the tile.
The modified thin set will stick to plywood...but you are much better off using the wonderboard, since it is quite stable compared to plywood. It will expand and contract with changes in temperature and humidity. The wonderboard wont. You sound like you are under control. Let us know how it turns out...and come back again if you have more questions.
