I don't think there's a phase where boostrap goes through the filesystem looking for *.info files and loading modules. I think it looks through the system table and loads modules, and the *.info stuff is cached in the registry or suchlike. The list of modules gets refreshed only when it needs to, which is either when you go to the modules page or use drush to list or enable/disable modules.
In particular, it looks like you're looking for _drupal_bootstrap_variables in Drupal 7, which is where module_load_all() is called. -- John Fiala www.jcfiala.net
