if I'm understanding your question correctly, this is the area behind the rear wheels. an area that is often rusted, particularly in snowy areas with salted roads. but even in dry areas, like southern california, the lower quarter area behind the rear tires is prone to damage and rust.
the trunk extension (inner quarter panel behind the rear tires) and the outer quarter panel are spot-welded together. they form a cavity. I nice place for small tools, housekeys, loose change, credit cards, and other small objects to collect as they fall from the trunk floor down into this abyss at either end of the trunk floor. Not to mention, dust, dirt and other debris collect in these areas, over time.
sadly, the areas around the back window and where the quarter panel meets the dutchman (trunk filler) panel and forming a lip for the desk lid, are prone to leakage. when it rains, where does the water go? onto the floor of the trunk, and then down into the aforementioned abyss.
combine this with the dirt and debris collected in these areas, and you get a wet soggy area that doesn't drain well, and in time, can rust through and show.
the trunk extension area is labor-some to repair, and I'm not surprised by your finding someone, somewhere along the way, decided to take a shortcut an minimize that pocket of rust-producing sludge on your car.
if you want to put it back, and make it correct, that's your right. from memory, this area is practically water-tight. I have cleaned these areas on prior cars. the two panels are spotwelded together, so well, one can fill the abyss with water from a garden hose and watch is slowly drip, drip, drip onto the ground. There is a removeable plug, about the diameter of a silver dollar, on the inner trunk extension, to help it drain and clean it out. but leaving it off seems a bad idea, because driving through any kind of water, be it a puddle or a rainstorm, seems to throw water from the rear wheels right onto that area.
that said, if seems wise to facilitate drainage from this area, so a weaker seal along the bottom edge of the abyss would be of great help. But again, it's unclear if water spraying off the rear wheels is a factor, if that area is left open. open to drain, and maybe open to fill from the rear wheels? It could be argued it is better to leave the area sealed and resolve the water issue from above.
this whole area is almost a design flaw of problems. most modern cars resolve this with a plastic inner fender well to divert water from washing onto the area. And most modern cars don't form this type of abyss or cavity going from the passenger area, minivan floor, or trunk all the way to the bottom of the quarter panel.
