I would just like to say that while i agree with most of what you are saying here i want to add a couple things.

Maybe your player just really likes dungeons and dragons and does not want to play some "bogus" homebrew.

Having a dm change so many things about a world that they based their character on knowing can be frustrating. If you are going to run a homebrew and know there are lots of changes to monsters or religions or environments.. i honestly think you should go over this with your players before they make their characters. This way they avoid building a character based on dnd lore. It also gives them a heads up that they wont be playing a more traditional dnd setting which if it isn't for them why are you punishing them?

I played with a dm who made so many homebrew mechanics and honestly.. it was a constant annoyance. In the end there were so many made up rules and so many times he told the group "no it does not work like that" or "no you can't do that" because of these new "awesome" homebrew mechanics he made up just to make things "ultra realistic" and in the end it was not fun.

Players OFTEN design their characters knowing what they have a good sense of. If you make a wizard you generally believe he/she will have a firm understanding of how magic works. And then you dive in a game where things are different and magic doesnt work the traditional way.. well you just took a huge spark out of your player by not telling them about this before they went and made their wizard.

Tl;dr Changing monster stats like hp ac and cr based stuff is no big deal and should be addressed with that player. But if you are getting into changing mechanics and lore i would suggest having a strong session zero and going over these ideas with your group. We all want to have fun.