I just went through this entire problem with my 96 SL2. I have torn the entire thing apart at all 4 doors and have a lot of thoughts on this.
The only one that was rusty was the right rear. The foam trim IS too short as was mentioned earlier and left quite a large opening at the top rear of the door.
Keep in mind though that the left rear weather stripping was the same yet there was no rust. This leads me to believe that something to do with the right rear door sill may have been overlooked during production. Especially if you consider that MOST people have the problem with this same door.
The door sill area is made up of 3 plies of metal. I noticed that it is the middle piece that disintegrates. I peeled the top ply back and the middle one was just dust that I cleaned out. The bottom ply, although rusty was still solid.
I'm thinking that maybe that area wasn't painted or sealed correctly and water runs down, gets under that plastic piece and soaks in between the plies of metal.
I pulled off the weather stripping and the plastic plate and I treated the area with POR 15 that I bought off the internet for 20 bucks. The stuff works great but I don't know about long term results yet. It's just a sample starter kit but it has more than enough of everything to treat the whole area and have lots left over. Probably enough to do the other doors if they are bad.
I used some black GE Silicone Extreme Conditions Caulk to stick the plastic plate back down and then I put a bead of caulk around the entire plate. I glued the stripping back down with Goop RV from Home Depot. I had to use a lot of duct tape to hold it down and then needed a lot of mineral spirits to clean up the duct tape glue.
I caulked all the other plastic plates and re-glued all the other weather stripping as well.
I hope that what I have done with this process is sealed all the water out. Only time will tell if it worked.
Andy