Also, rather than confirming via a link which then takes to the webapp for the confirmation, why not confirm them using say a reply email? this way the user doesn't have to leave their mailbox (more convenient for a mobile user)

Historically, because parsing email is hard, because a lot of reply emails will fail to include your magic verification token in them, and because (if you don't use a magic verification token) spoofing email addresses is trivial.

The easier solution is to simply not verify email addresses.