Frankly: I have no damn clue what I am doing, I am just following Internet tutorials.
When it comes to the lack of the -H option: I followed the Certbot instructions. I don't know what -H is for. And I ... somehow didn't saw it mentioned in the warning message. Whoops.
When it comes to the directories ... it fixed the error of "not-permitted" and According to the linked article, it's because of MacOS and its security features.
And well it works so... why doubt it ?