tobik added the comment:
Yes, the bug still exists and all Python versions are affected.
We patch them all in FreeBSD Ports:
https://cgit.freebsd.org/ports/tree/lang/python36/files/patch-Misc__python-config.sh.in
https://cgit.freebsd.org/ports/tree/lang/python37/files/patch-Misc__python
New submission from tobik :
When symlinking python3.6-config to another location, it starts
outputting bogus paths. It's convenient to symlink the system
python3.6-config to somewhere else in PATH to make sure the build
of an application with a hardcoded use of python3-config is usin