Mysterious user registration hook?

There seems to be much confusion over how and why WP overrides various attempts to create custom new user registration pages. I’ve been poking through the code, but can’t seem to quite understand where and how it is performing these calls.

I am attempting to create my own new user registration page which has many different options and boxes for visitors to fill in during the registration process. The problem is that WP keeps ignoring my attempts to override the default wp-login and/or wp-signup files.

Is there a secret to this madness?