Simon,
The post you refer to, for logging a Joomla (non-Facebook) user in with the SCLogin module, that will respect the different CB settings for username type. We get a lot of feedback from users and are always trying to improve our integration where we may lack.
As for your specific question, we do use CB's API when saving the user. However, JFBConnect first creates the Joomla user in the standard way. Then, we call the CB function "saveSafely" with a parameter of 'edit'. This is because the user has already been created (even if it was just moments before) and isn't a real registration. The 'edit' process does trigger different CB events like "onBeforeUserUpdate" and "onAfterUserUpdate", but it does not trigger the "onBeforeRegistration" event.
For JFBConnect/Facebook functionality, we more or less have to do it this way due to processes that we need for proper integration with Facebook (the Joomla user creation processes which are shared for a lot of different functionality) and limitations in CB's registration process (which is very rigid and is not welcoming to other extensions trying to use it).
Hopefully, you can switch your plugin to use the other trigger events within CB mentioned above. We can also help you with some code that could actually tell you if it's a JFBConnect registration that's actually occurring, if that would help. Otherwise, you could also move to using a Joomla User plugin which would definitely work with the JFBConnect registration process. It would also work with any other registration process because it's the standard way to do things.. which isn't what CB does. Not that that would help you necessarily.
Anyways, hope that helps explain, but if you have other questions, just let us know.
Thanks,
Alex