I just found myself going down a 15 minute rabbit hold to learn the answer to that question. It's interesting, but I'm not sure it's useful to that many people. OTOH, maybe it helps demonstrate why you want to be very, very sparing with hook_boot().
Found the answer on SO, btw, after I gave up on finding it in the source:
http://drupal.stackexchange.com/questions/101369/why-drupal-changes-the-module-system-table-bootstrap-value-after-i-set-it-with