The problem can be reproduced as follows:

Run the following commands to install python with a site configuration file that installs the libraries to lib64:

  export INSTALL_DIR=/some/path/to/install
  mkdir -p $INSTALL_DIR/share
  echo "test \"\$libdir\" = '\${exec_prefix}/lib' && libdir='\${exec_prefix}/lib64'" > $INSTALL_DIR/share/config.site
  ./configure --prefix=$INSTALL_DIR && make install

Check that the libraries have been installed to lib64 and that python fails to find them:

$ find $INSTALL_DIR -name lib-dynload
/some/path/to/install/lib64/python3.6/lib-dynload

$ $INSTALL_DIR/bin/python3 -E
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Python 3.6.0a4+ (default:98a57845c8cc, Sep  9 2016, 15:34:27) 
[GCC 6.1.1 20160707] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import base64
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/some/path/to/install/lib/python3.6/base64.py", line 10, in <module>
    import struct
  File "/some/path/to/install/lib/python3.6/struct.py", line 13, in <module>
    from _struct import *
ModuleNotFoundError: No module named '_struct'
>>>