The auto-update option you see in the config file actually refers to a built in option that once activated will let the plugin check if a more recent version is available and prompt the user to download the last version if necessary. If you deactivate this option you will have to build your mechanism outside of the plugin that will determine whether or not the plugin your users are using is up to date and if they need to download the new version.

This system is designed to provide a simple, but robust, (auto) update system for end customers, thus reducing the manual  need to support the plugin.

At the time of build, you will be asked for 4 URLS to allow  as part of configuring the plugin: 

At every start, the plugin will check the "Current Version URL", and if the version received is higher than the currently installed version, a popup will be displayed.

When the "Update" button is clicked, the installer for a plugin's new version will be downloaded.
The user has to manually start the installer and restart their browser for the new version to be available to the browser 

It will look like this :

Customers are free to turn off auto-update at build time.
If so, they will have to design their own update system. This will give them more freedom, in terms of workflow, and look&feel.
Relevant Javascript APIs are:

• [pluginElement].VERSION : returns the version number of the locally installed plugin.
• [pluginElement].COMPANY : returns the company name of the locally installed plugin. Make sure you don't update the free plugin, or some other plugin.