Vim embedded PYTHON_HOME when vim is built. In case of Homebrew’s Python, it is real prefix, not opt_prefix.
no module named site (on Python 2) or
no module named encoding (on Python 3) error and vim is crashed.
It was fixed in upstream vim, in 8.0.1683. Vim doesn’t embed PYTHON_HOME unless
--with-python3-config-dir configure option is used.
Currently, vim and macvim needs revision bump after every Python upgrade. (FYI, macvim revision is not bumped after Python 3.6.5. So macvim crashes for now).
It means revision bump for each Python upgrade is not required after vim is upgraded to 8.0.1683+.
Macvim merged the fix from vim, but doesn’t have new release yet.