quick question. If silicone caulk is put in a 1/4" plywood floor expansion joint where the plywood meets the wall will the silicone compress enough so it doesn't effect the expansion of the wood without pushing up the floor covering?? I'm curious because of a tile floor i'm installing in a bathroom. The plywood subfloor is new and i'm concerned that when water gets into a grout joint and through cement board it could drip through expansion joint and onto ceiling underneath before it has time to evaporate.
The place to stop the water is before it reaches the plywood, not after. If the plywood gets wet it will not dry out, it will rot. Seal the grout. However, to answer your question, the silicone will not cause buckling of the floor.
Sounds like you might be a little light on the substrate for tile, you've got 5/8" or 3/4" plywood sub and then 1/4" plywood? You should really have a minimum of 1-1/4" of plywood in most applications. (Standard 16" o/c joist spacings). Did you already or are you going to thinset under the cement board?