The change to _base_executable is the real problem. Venv creates the correct directory structure if I add a sitecustomize.py to the python path that sets _base_executable to the correct value.

# sitecustomize
import sys
sys._base_executable = sys.executable
# EOF

Is sys._base_executable updated after running getpath.py? On first glance getpath.py does update config['base_executable'] and _PyConfig_FromDict reads that value back, but that's based on a quick scan through the code. I haven't tried debugging this yet.