Adding

_OLD_VIRTUAL_PYTHONPATH="$PYTHONPATH"
export PYTHONPATH="$VIRTUAL_ENV:/path/to/project:$PYTHONPATH"

and the corresponding revert in deactivate()

if ! [ -z "${_OLD_VIRTUAL_PYTHONPATH+_}" ] ; then
    PYTHONPATH="$_OLD_VIRTUAL_PYTHONPATH"
    export PYTHONPATH
    unset _OLD_VIRTUAL_PYTHONPATH
fi

to the venv activation script and running run.py directly from entry_point (in that way specifically, not from project root) did the trick while being the least intrusive option.