Actually I found something in the release notes for SG Desktop.
Specifically:
V1.6.1
What is new?You can choose which version of Python to run Shotgun Desktop under. When running the Advanced Project Setup in Python 3 mode, projects will be configured to use the built-in Python 3 interpreter. Note that once setup, a project configured with Python 3 can still be used by a user running a Python 2 version of Shotgun Desktop and vice-versa.
To select which version of Python to use on startup, set the
SHOTGUN_PYTHON_VERSION
environment variable to2
or3
.
So it seems like something is set after the advanced project wizard to launch a project in python 3 mode.