To me, the fact that you are directed to install Homebrew to /usr/local is wrong since there's no guarantee how /usr/local is going to treated by Apple in the future and this is now an example of that. The only directory that Apple, probably, doesn't have control is your home directory.

I've been using homebrew for a long time without issues because, in my opinion, I installed it on ~/homebrew. I wonder why is that so difficult for others to use.