i would be surprised if this is true.  The CB trunk has a lot of wood in it, and if it was built without wood, in the same mold, it would need a lot more fiberglass to fill the mold out.  Sounds like a wives tale, or a psych job by your competitor in your club.
There may be some small differences in how the Customflex boats were built, but Sandy was pretty careful about not having licensed builders that would cut corners or build out of spec boats.
The two differences I have seen on CF boats is that they come with different trailers, and some have a "bow eye" that is on the nose, below the regular bow eye, that protrudes.  We have made it a rule in our club to take those off, as they are very damaging to another boat it you hit someone, much more than the vertical bow trim that is standard.
By the way, all boats flex to a degree.  If your floor feels really soft, I would check for wet balsa wood, or if the floor is leaking it is possible that the wood in the trunk is rotten.  It's much more likely that the balsa in the floor would be wet, and thus feel soft.