In an Aegir platform how do I change what modules drush enables when a site is created
Both requirements (auto enable modules and autopopulating users) can be done by Drupal install profiles or distributions. Install profiles are in Drupal, not in Aegir, but fits perfectly to Aegir.

In short, I recommend you to compile your install profile and use this profile in Aegir.

See more: http://drupal.org/project/distributions