Calling JavaScript by plugin vs wp_enqueue_script ()

The registration and queuing of scripts and styles is definitely the correct way to include these assets. This approach allows much more flexibility (conditional loading, declaration of dependencies) and helps avoid duplication of assets and conflicts.

Including CSS & JavaScript

I checked the code of the WPBeginner add-in Insert headers and footers and does not make any conflict resolution or verify the duplication.

So, yes, the complement route creates a greater likelihood of conflicts and no, it does not solve the problems for you.