At startup the Python interpreter has a minimal system path from which
it automatically imports site.py before doing anything else. This
can be skipped with the -S option. Running the module directly
(python3 -m site) gives information about what it's configured; this
will give correct results with -S because it checks itself to see if
sys.flags.no_site is set.
Full details of the initialization are given in both the source and documentation (v2 docs). See also Stack Overflow What sets up sys.path with Python, and when?.