The reason for cbu installation over plywood is so that you have a surface that is compatible with the tile, expands and contracts the same way as the tile, so it all works together. What actually happens over time (and it doesn't happen quickly), is that since the cbu (or tile if adhered directly to the wood) expand and contract at different rates, and the bond can be broken. So, if you follow the manufactuer's instructions and use an unmodified thinset, it has no elasticity to it, the bond will break and you have the cbu and tile disconnected from the subflooring. When using the specified fastener, what really happens long-term is that the tile and cbu move, and actually crush the cbu around the fastener so the cbu and tile are a floating floor, held down by the fasteners. this motion is very small, but exists. If you choose to utilize one of the approved methods of tiling directly to (two) layers of plywood, you are required to use a highly modified thinset (which has a little give to it). Use a lower-compliant thinset, or have a less than perfect installation, and you risk failure. There are organizations whose sole purpose in this is to evaluate tiling installation methods and come up with methods that work long-term, under adverse conditions. The manufacturers run their own tests. Trying to second guess all of that research with a few personal experiences is fraught with room for failure in the general use situation. Plus, except maybe in a home situation where you DIY, this failure can take years, often gets disconnected from the installation method utilized...in other words...things could fail, and you would never know why or if.
RTFM, and follow it. You might get lucky, you might not, if you don't.
The thinset in a cbu installation is there to fill voids, NOT to hold the panel in place. The fasteners hold the cbu in place, and a second purpose of the fasteners is to smush it into the thinset to minimize the notches (i.e., spread them out to fill in the gaps - providing the desired 100% coverage).