JAYCO got back to me about the floor and here is what they said,
"I completely understand the question on the floor as I would also question it. There has been no issues brought up concerning the floor on your model, I would suspect your feeling a cutout in the floor for some component and they do there best to fill it in so its not noticeable but the areas can feel soft when putting pressure on. I would not think it is anything safety or water damage but just to be on safe side once your done with the trip you can have it inspected to be reassured."
Since it's above the wheel opening, it probably is due to lack of support. I will have it checked out at a later date.
2016 Greyhawk 31DS
2016 Chevy Equinox LX
Blue Ox Baseplate w/Aventa LX Tow Bar & KarGard II Deflector
Blue Ox Patriot Brake