Can a manually uploaded plugin be made to track updates from the WordPress.org plugin directory?

As long as everything was made according to WP best practices all your manually installed versions will update the same as the ones installed from wordpress.org.

The updater looks at many things to identify your plugin. However, the most important is the plugin URI (you can change the directory of many plugins and they will still work), but the name and slug are also checked. After WP detects that it has a matching plugin it will check the version and send out update information as needed.

Edit 1 Based on a little more research, I see that the update check seems to be done by wordpress.org at this url: http://api.wordpress.org/plugins/update-check/1.1/ to see how the call is structured you can look at the core code for wp_update_plugins().

The reason your manually installed plugin will update is the same as the reason you can manually download and install a plugin from wordpress.org and see it recieve updates in the wp-admin.

There is a way to have a privately-hosted plugin folder that will get updated via the normal Admin, Updates process. It's a bit complex to set up, but I have done it.

The info is here: https://github.com/YahnisElsts/plugin-update-checker#github-integration .

I modified it to use a private area of a domain I own to be the code repository.