In reply to Jeremy Saxey.

I cannot speak with authority regarding WP Pusher, but GitHub Updater requires the developer of the plugin or theme to opt in to automatic updates by inserting a header into their code. It is also open source and developed on GitHub.

While you can remotely install any plugin or them from GitHub or Bitbucket only those repos with the designated header will be receive automatic updates.

My supposition is that WP Pusher stores the repos it installs in the database so it can access them later for updates. GitHub Updater only stores transients.

GitHub Updater is free while WP Pusher is a paid service for certain features.

If you have any specific questions I can answer, please let me know.