I think you misread what I was getting at. In this scenario Emacs doesn't call the package manager - if emacs manages packages it does it for itself in elisp. B

I think you misread what I was getting at. In this scenario Emacs doesn't call the package manager - if emacs manages packages it does it for itself in elisp. But it doesn't matter to emacs whether the package was installed from an elisp program or from a .deb file, because the end result (predefined format in predefined place) is the same regardless. So you're free to use, or not use, the package manager of your choice. Or mix them.