I have a few soft spots as well (2019 Entegra Esteem 31L). I didn't notice it on the PDI since I was wearing shoes. It seems I can only feel them barefoot. I can't imagine it's from water, as the rig was on the dealer lot for only a few days and since I picked it up, it hasn't rained!
After crawling around underneath the rig this weekend, I did find a few very small rips in the black plastic sheathing that's covering the plywood underneath the rig, around the wheel well. I'm guessing maybe a rock was thrown up and nicked the plastic. Seems like there should be something there beyond the thin plastic, around the wheel wells at least!
I see that infomercial about flex seal, wondering if I can spray that stuff over the plastic above the wheels in the wheel well?