As far as I understand, the Dead Sea is the new timeline that Crono and the gang created after the finish of CT, from 1999 on (with the assumption Lavos was defeated in 1999). All of the matter there is under a vaccum-meld-freeze kind of thing because most things are static (the water, for example...), and the whole area is a conglomeration of the whote timeline mashed into one area as a demonstration of what will happen in the future in Home World if Serge does not straighten out the dimensional distortions.
As for how the blackbird scrap would end up in this timeline is a good question. I'm not sure the ocean palace wreck or the mammon machine would be a plausible cause since the blackbird appears after the ocean palace is destroyed...
I honestly have no idea how it would end there. o_o But I saw it!
The Dead Sea is the whole world and timeline which was disgarded thanks to an event in the past. It's all condensed. So if the black bird survived the crash and fell to the bottom of the ocean, part of it could be there.
Also, The Dead Sea (if it is only one true timeline) is the future that Crono and co avoided (the one where Lavos reigned). But then again, like I said, it's all of them combined from all of this time travelling mess. That explains why Company 2400AD is there since Chronopolis' meddling caused that timeline to be rewritten too.
