

Also, even within the one option, if at some point I upgraded my Linux system and I got an empty /var/www directory, it would never in a million years occur to me to say “Well that’s stupid I don’t want that directory” and remove it.
Because frankly you don’t know enough to know any better. Sorry if that sounds condescending, but it’s the truth. You should be able to delete /var/www without it causing any security problems. That you don’t know that isn’t your fault, it’s experience.
Nothing else you said mattered. 🤷