Hi Damian,
thank you for your e-mail!
That script is stable, no bug reports in a while, stem is working fine. :)
That authentication line and "password" is only in there to make stem happy. help_check_tor_bootstrap.py/stem isn't "really" using Tor's control port. It connects to Control Port Filter Proxy (CPFP) [1], which does the real authentication. CPFP - a whitelisting proxy - accepts any password, authenticates to Tor using cookie and filters out potentially dangerous (for anonymity) commands (such as getinfo address).
Cheers, Patrick