The OP uses (set-frame-parameter nil 'fullscreen 'fullboth).

In contrast, I use (set-frame-parameter nil 'fullscreen 'maximized) leaving OS X's menu bar and Dock on the screen.

I do not know if Homebrew package `emacs` has been fixed because these years, I only ever install Homebrew package `emacs-mac` (a.k.a., Mitsuharu Emacs) but it used to be that one had to install Emacs.app via `brew install emacs-mac` instead of the conventional `brew install emacs` for (set-frame-parameter nil 'fullscreen 'maximized) to automatically and cleanly occupy every screen pixel except for the pixels needed for the menu bar and the Dock.