Yes, the idea is generally targeted to multistore installations so we can achieve better coherence with FO branding and not use style-neutral templates.
But it can also be useful for merchants using various modules from separate developers to track, detect, and unify them in one style. For example, currently my revws emails are quite different from my core ones. Yes, you can do that when using one shop by changing the module email template, but you have to keep a map of the modules that have emails and track this on every module update. Using the module, you will create a module email template override and use it instead of the standard one.
Can you give some screenshots of the empty templates you use?
The inspiration for this module came from one long forgotten one my theme developer supplied, but it is no longer packed with the theme, I even failed to find it in old backups of the template so no logic is shared at all.