To reiterate, So what would be the currently best method of creating a portable workflow ?
Looks like /usr/bin/env python3 is not the way to go since default paths are not including /usr/bin/local which brew populates with python3 which appears to be the most common way to get python3 into OSX.
Furthermore, changing OXS's default $PATH looks like a bad idea both for portability and for OSXs apps predictability.
Executing the python script after setting PATH inside a wrapper shell script is the quickest workaround, am I right in my understanding ? ( Although it does not fully solve the issue since a user may need to change the PATH in case it's setup is not using brew )