Hi,
They are separate but related things.
CustomRegistrationPage configures the link so it points to your custom register page, if you don't want it to do that then don't configure it.
RedirectRegistrationPageToCustomPage forces the built in /Secure/Register.aspx page to redirect to your custom registration page. That way if a user gets to the built in registration page by url instead of by the register link, it will redirect them to your custom page.
So if you are using a custom registration page you should use both settings, if you are not then you should not use either one.
Hope that helps,
Joe