When building modules and trying to set the proper linker flags for the library runtime path, the detection of the compiler is wrong. the issue: 
https://bugs.python.org/issue20767 was showing the issue and imho badly fixed.

Clang behave like gcc regarding how it passes flags to the linker: -Wl,... so clang and gcc should be treated exactly the same way and no specific code should be added for FreeBSD

Here https://github.com/python/cpython/blob/master/Lib/distutils/unixccompiler.py#L237, it should accept both clang and gcc,

This block https://github.com/python/cpython/blob/master/Lib/distutils/unixccompiler.py#L230 should be removed

The issue is not only on FreeBSD but on any system which compiler is clang. side note, the detection of gcc looks at first glance wrong, as on many system gcc is installed as cc sometime.