I think the problem here is that as the OP mentioned, win_add2path.py doesn't add the directory if it doesn't exist, so if you run it immediately after install, it won't add the directories that don't exist yet. And because it's setting the registry entries to make the path changes persistent, you only run it once and don't rerun it after those directories are created. Although if you did, that would fix the problem...

Maybe win_add2path.py should add the directories even if they don't exist? It only means removing the isdir check from the line

    if path and path not in envpath and os.path.isdir(path):

I don't really have a feel for whether that would be a good idea. I guess the only harm would be a bit of clutter on %PATH%, and probably no-one cares about that...