I haven't noticed any rot on my 2006 Explorer 1700 Sport. Once a year I give the "carpet" a scrub and let it sit in the sun tilted so all the rise water runs out. I clean the bilge also. I haven't noticed any trapped water so I hope by design it's all running out. I always leave the boat tilted to the stern as much as possible with the drain plug out. Just condensation can build up and probably create a soggy environment under the cover. Whenever I store it I leave the cover open in a few spots in the garage so it can breath and also crack the garage window so there's always fresh air to help keep it dry. Carpet may be more forgiving in terms of letting the plywood breathe but can't say for sure. Do you pull the vinyl floor up when storing to let it breathe? That should help. I'd take a towel and soak up the water in the base wells if that's getting sucked up by the plywood. I'm not sure if there's a magic formula, but "marine" plywood does seem to rot over the years and it's not an easy job to replace.
I have no warranty experience since I bought my boat when it was 5 years old and didn't want to pay to transfer the warranty. I would think Lund should cover your floors if they were well cared for.
Good luck, keep us posted.