I like using Pydev for Eclipse, so when at first I had to set up the Pydev interpreter for ArcGIS Pro and the conda install, I ran into a snag.
In Eclipse (or Jupyter, or other) you can choose your python install and manage your python path. This is pydev for eclipse Luna. Eclipse - project - properties - PyDev - Interpreter/Grammar settings:
I changed my grammar version to 3.0, and click to configure an interpreter not listed:

Here is my default interpreter for my ArcGIS 10.4.1 environment:

I created a new environment and chose the python.exe at the "propy path" documented here
using-conda-with-arcgis-pro
at the ArcGIS\Pro\bin\python\envs\arcgispro-py3 directory:

and now my pydev for eclipse works in the ArcGIS Pro 1.4/conda interpreter.
What threw me off originally, and prompted this thread: python.exe exists in multiple locations under my Pro directory, and the envs directory was not the first place I found a python.exe for eclipse to use.