I used to park my RL with the nose low and found my truck full of water. The dealer showed me a series of drain holes around the perimeter of the trunk; they were plugged with tree and pollen debris. Even after this knowledge and trying to keep them clean it would leak.
My ultimate solution was to park with the nose high and continue to monitor/clean those holes.
Additional note: I believe the bed is plastic and if correct rust will be very Very VERY slow in forming.
You should also make sure the channels for the trunk on the bed floor stay relatively clean and clear of debris - those channels help the bed drain - if they get clogged , water can back up into the trunk and soak anything in it - I found this out the hard way after a bad rain storm and several weeks without opening the trunk - had to toss a very moldy infant stroller...
The bed floor, cab wall, R/L sides and inner tail gate panels are fiberglass. No rust worries there. However, everything behind them and all mounting points are metal where rust can get a foot hold. Recently had everything but the floor out of my southern California 06, no sign of rust anywhere.
There are a series of 8 weep holes at the front edge of the bed floor, (estimate 1/4" round) where it meets the cab wall. They are intended to allow water collecting there an escape path. Unless they become debris blocked (which is very likely pending local environment). If you have issues with standing water, remove the two upper cargo cleats (4 - T50 Torx) and six T45 Torx bolts holding the bed wall. Pull it gently towards you and wiggle upwards until it come free. Be careful, the fiberglass panels are tough but scratch easily when one fiberglass panel rubs/bumps into another. Set it aside and clean the holes seen here:
There are similar weep holes around the trunk opening, just below the gasket. Same issue/benefits there. Keep them clean and water should flow freely. Any other water is dealt with via gravity and air motion.