having ridden in the rain... that area becomes an indoor pool... there are no drain holes
With my original chassis I silicone sealed between the aluminium floor & chassis rails & it stayed dry even though I travelled some very wet roads. When I got the replacement chassis MMC did not replace the sealant nor the sealing tape behind the seats. I did not reseal & the floor stays dry, I did re-tape behind the seats to cut down the dust.
Craig have you found the removable panel above the pedals to aid access? WD40 will not prevent rust, ACF50 will inhibit it, I use it on the front suspension.