> Python's SSL isn't using that.  Python is taking in one big text file 
> of SSL certs, with no link structure, and feeding it to OpenSSL.  

Python's SSL is not "taking" anything:

>>> r = urlopen('https://www.verisign.com')
>>> r.read(10)
b' <!DOCTYPE'

It's only if you feed it that particular CA file that you get the issue:

>>> cafile = 'cacert.pem'
>>> r = urlopen('https://www.verisign.com', cafile=cafile)
[...]
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:600)>


You can *also* feed it a CA directory by using the "CApath" argument (*not* "CAfile").

Now it remains to be seen why "openssl s_client" works with the file nevertheless.