Hey Shovelshort:
I would seal the bottom and back of the vanity with 2 or 3 coats of spar varnish. Then procede with the tile and wall finish however you please.
Likewise on the toilet flange, use whichever method that will give you the best anchorage. When you are ready to set the toilet you can buy a closed cell foam gasket, $3 or less. It will be resilient and maintain a seal for years, whereas the wax bowl ring will leak with the first wobble of the bowl. It happens in the best of instalations. To help with the wobble you can cut some pieces of PVC pipe (cut off the end at a very slight angle) and place them to stop any wobble. Then liberally caulk the bowl to the floor with white tub and tile silicone caulk.
Glenn
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