As to your question as to if this is a custom Python install - I would assume not? If it was, then that would have been set within the instructions for creating that python:3.6-stretch image. It does appear that Python is aware only of packages in /usr/local.
Re: my original issue. It turns out the ModuleNotFound error stemmed from /usr/lib/python3/dist-packages/ having older versions of Numpy and Scipy. Adding the PYTHONPATH first, then upgrading Numpy and Scipy (numpy==1.14.0 scipy==1.0.0) allowed me to import graph_tool successfully (and have it be able to import the various dependencies it was err'ing on before).
If you have thoughts about the different versions of Python and some cursory familiarity with the configuration of that Python 3.6 image; I'd be interested in finding a less awkward solution than what I did to get graph_tool up and running. Otherwise, I'd label this issue as "resolved." Thanks.