other methods of sending the email may work, but I cannot say if they will for certain.
the key to double option is this:
on registration, a new record is created in the users table. the verified column is set to 0 and a random string is inserted to the random string column.
an email is sent to the user that just registered with the Primary Key value and random string as querystring variables in a link to the confirm page.
the confirm page uses the querystring variables to update the verified column of the users record.
as long as your other email method allows you to modify the email that is sent and add the link to the confirm page with the ID and Random string, then it should work.
I know that GoDaddys form mailer script instance will not allow this sort of control over the email message. I'm sure there are other methods out there that have the same restriction. I'm also sure there are other methods that will work.