I don't really understand what you are trying to do.
If you want to modify an extension, you will have to fork it (make a copy), makes changes, re-compile its javascript and load it through a custom Composer repository. If you modify an extension in the vendor folder, your changes will be lost whenever you perform updates.
For changes that are only visual and can be done with CSS, you probably don't need to modify the extension at all. Just add your additional CSS to the admin panel "Custom CSS" to override the default CSS from the extension.
Even for javascript changes, you might be able to create a new extension that changes the behavior of another extension, that way you can still update the original extension without having to port your customization every time you want to update.
