The upload folder works fine until you restart your client, pretty sure theres a way you can store the information in a local file until the download finishes completely or the parts are not needed anymore. But maybe the DC protocol doesn't have the support for this. :/
I think this would encourage more users to pack the files they share, not sure, but I think thats the main reason behind auto-sfv checking being implemented was for packed files, which leads to multi-sourcing, which is constantly mentioned on all Direct Connect related forums I've been to. Most just don't understand it, I had to think about it for awhile until I finally got it.
In my opinion the file trees and auto-sfv makes DC unique and my P2P program of choice, its starting to look a bit like FTP sites. If users would stop extracting files it would be almost identical to sites. Just a big community of sites