This question isn't to the community as much as Esri staff involved with ArcGIS Pro development.
I gotta say, there are times I really dislike Esri having two Python APIs that don't appear to coordinate much at all in terms of development. Case in point, I want to Copy To Data Store—GeoAnalytics Tools | ArcGIS Desktop from a stand-alone Python script, but our organization's internal Portal/Enterprise is PIV enabled and enforced.
Looking at SignInToPortal—ArcPy Functions | ArcGIS Desktop, you have one authentication option, username and password. The documentation does at least acknowledge some of the limitations:
Portals that use Integrated Windows Authentication are not supported; username and password are required parameters.
The kicker for me is that the ArcGIS API for Python supports many more authentication options with arcgis.gis module — arcgis 1.4.1 documentation .
So I can use my PIV to authenticate with Portal/Enterprise using ArcGIS API for Python but not ArcPy with ArcGIS Pro? I really hope I am missing the obvious.