Thanks for the question and feedback. First, keep in mind that Sync is a beta product and we’re still actively building it, things are evolving every day. We’re investing a ton of time and money into it, there’s a ton of great stuff happening and more coming.
As for your question, yes, we're planning on releasing a version that will allow for you to use your own tracker - unfortunately we don’t have timing yet for that but it is in the works. We're working hard to make a great product and to support everyone as best we can.
Also, we do have a dedicated forum for the Sync API http://forum.bittorrent.com/forum/106-developers/ in case you have other questions/comments. Thanks!