Spare Tire problems of the 2008 Honda FIT

Vehicle parked during rain event, noted heavy leakage into spare tire well and passenger side rear floorboards. It appears to be coming from multiple sources. Windows heavily fogged/iced up from moisture in cabin. This happened twice this month. Secured dealer appointment, but when I arrived I was told that I have to bring it in when their leak specialist is at the shop (why does Honda have a regularly-scheduled leak specialist??). I was also told that I have to pay for diagnosis and repair since the vehicle is out of warranty. I have never had a car that leaked water. The Fit now has rusty metal parts, wet carpet, and possibly damaged electrical components from water infiltration.

Water in spare tire well. Originally thought water in the tire well was due to hatch opening during rain/snow, but since vehicle was not used for a week during heavy rain, this must be due to a leaking window seal.