"The "over-tightening rigging" sounds like a red herring " Not necessarily. I've seen the head doors jam in a number of boats because of over-enthusiastic rig tightening. Among other things.
If there's a solid filler under the mast (as there should be) and there's a compression post/beam/system under the deck (again, as there should be)...You'd have to do a real gorilla job to compress a good marine grade filler under the mast. But I think we've all met marine gorillas, I just can't remember the proper Latin name for the species.
"Yeah just stick a plate under it to regain the thickness and slack off the rigging" could actually be simply good advice, once upon a time that's how things were "made do" done. OF course, as a card-carrying cynic I'd be reluctant to do that without opening up the deck and actually SEEING what had happened inside it. Or getting something else (ultrasound?) to see inside it without peeling it open.
It sounds like this is worth a longer call to Beneteau, to ask them for more information on the larger picture.