I am also running some pi's with bittorrent sync. From my experience with large epub-collections (with files from about 200kb to 5MB) it is best for a large amount of files to be tar'ed first if possible. writing a small bash-script for this with a md5-comparison to find changed files in a folder should be done quickly.
If someone just wants to replicate the function of dropbox to drop files in folder and get a sharinglink for them "in the cloud" then u could try pydio (formerly known as ajaxplorer). free & open source. this in combination with the possibility of adding bittorrentsync-keys as presented by the threadstarter would be superior. (maybe make a fork of ajaxplorer?)