Exclude mu-plugin from Bedrock Autoloader

Is it possible to exclude specific plugins from being loaded via the Bedrock Autoloader? I have a couple sites on WP Engine, and they load a strong passwords plugin as a mu-plugin with an entry point .php in the /mu-plugins folder and a separate folder for the main plugin. Their entry point loads the plugin, and then the Bedrock Autoloader comes by and tries to load the plugin again (or the other way around - but their entry point doesn’t check to see if it’s already been loaded anyway).

Changing their entry point is not possible, as their systems automatically replace any changes to this file. I just want to tell the Bedrock Autoloader to ignore this particular folder.

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