Please keep posting photos and results from talking to Toyota and FWC. Here is what I can see for now...
1) You said it was overloaded. I fully expect the Toyota Service Rep to take the truck to a set of scales and weigh both axles and compare that to what the VIN tag says the truck is rated for.
2) If in fact it is overloaded, I think you voided any responsibility on their behalf.
3) I don't know what the FWC guys will say, but there are an awful lot of posts on WTW that indicate suspension tune-ups are needed/required for overloaded trucks.
4) However...While I am not that familiar with the FWC installation methods, check inside for some metal gusset plates that the eye-bolts pass through before bolting down inside the camper. They are strongly suggested for older rigs as plywood ages and gets wet/soft.
5) If you noticed an inordinate amount of SWAYING of the camper in the rear of the truck, then that swaying movement is transferred to the bed of the truck. That would tend to work the attaching points of the bed to the frame. If subjected to enough of that working on the metal over time it would fail/crack as your photos show.
6) I don't remember if you bought the truck new, so if not....check CARFAX to see if there are records of damage that would account for the overspray under there.
7) Before going to Toyota, I suggest you weigh the front and the rear and both axles and compare the results to the VIN tag.
In the end, I think Toyota won't be of any assistance. The damage is not due to rust unless you can show that the rust is a widespread problem on the truck bed which from the pics does not seem to be the problem. FWC may point out that all models like yours installed in Toyotas like yours have been OK but that many owners did beef up suspension to AVOID the sway which in my opinion is what caused this failure.
You may be left with having to remove the bed and have a qualified welder fix the problems and add some substantial gusset plates where the eyebolts come through. Then you need to address the causes of SWAY....that may be as simple as slowing down or doing suspension upgrades and tire upgrades to your truck.
Another option is to buy a truck with GVRW and axel ratings that can handle the camper....