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Admin Tools does not update anything, nor does it have any features which can enable, disable, or otherwise affect the update of any extension including but not limited to plugins. Whatever you are talking about, it has nothing to do with Admin Tools.

With that note your initial request makes a lot more sense. Please remember that auto-updates ARE NOT handled by Admin Tools; they are handled entirely by WordPress. We have marginal control at best over what WordPress does with automatic updates, as you will see below.

The Plugins feature under "Auto updates" merely responds with false to the auto_update_plugin filter event which is sent out by WordPress right before it tries to update a plugin automatically. As you see in the link I provided, returning false from this filter will stop WordPress from automatically updating any plugin, regardless of the plugin's auto-update settings.

When you have enabled this feature Admin Tools sets up a filter hook returning false when WordPress runs the muplugins_loaded event, very early in its boot order. The code Admin Tools runs in this case is the following single-liner:

add_filter( 'auto_update_plugin', '__return_false' );

That's really all there is to it. It's simple, it works, but this being a WordPress filter hook which is set very early in WordPress' boot order it does have some inherent drawbacks about how much it can control, and even whether it can control anything at all.

First of all, it will only work if the wp-content/mu-plugins/admintoolswp.php file is present, it is readable by PHP, and the Admin Tools plugin is enabled. This file is created when you install Admin Tools. If you delete it, or change its extension, the early-loading features in Admin Tools won't be loaded – and that includes the features controlling automatic updates. You need to check that before reading anything else below.

Being a filter hook, it's not set in stone. It is perfectly possible that another plugin calls WordPress' remove_filter to remove the filter just added by Admin Tools. If that takes place, the setting in Admin Tools will have no effect. There are many plugins which could do that, especially security and site optimization plugins which have their own controls for these “hidden” WordPress auto-update features.

Further to that, if you are using a third party service or software to manage updates on your site –such as but not limited to mySites, Watchful, MainWP, or Akeeba Panopticon– this feature in Admin Tools will have no effect. These third party solutions do not obey WordPress filters, which is kinda the entire point: you disable auto-updates in your WordPress site, then you use the third party solution to have fine-grained, centralized, and possibly automated updates across your sites.

Moreover, this will not have any effect to manual updates. Manual updates can take place either by the user clicking on the update link of a plugin in the Plugins or Updates page, or by uploading the same or a different version of an already installed plugin from the Plugins, Add New page, or through WP-CLI. This makes perfect sense, as they are supposed to be the manual overrides to disabled automatic updates.

Finally, there are plugins which self-update themselves without being bound to WordPress' filter events. Again, these plugins' update behavior will NOT be controlled by this Admin Tools feature.