In your case, a tracker is needed and is used of course. Next, an answer to "how" may be well-known technology of "hole punching": http://en.wikipedia.org/wiki/UDP_hole_punching
This is easy. Make new user. Login. Run BTSync. You have 2 BTSyncs running in separate processes, now you can emulate syncing of 2 hosts. Just checked it worked very well on Windows 7.
@nils: Ok, BTSync for windows is 32-bit and the author said: "sync a windows directory". Make conclusions. The author can dance with other settings, but it won't help. Problem is solved. You can't sync so many files on 32-bit app.
From unofficial FAQ we know that "if you're monitoring/syncing 1 million files, you will need around 300-400 MB of free memory". BTSync is 32-bit, so, it can only use ~2 GB of RAM. Therefore, the maximum amount of files is limited to ~6 million.