<< The continued use of e-ticketing has been approved by the FAA.
Customers traveling on e-tickets will need to provide documentation of their purchase as proof of travel in order to pass through security checkpoints. >>

Having an e-ticket doesn't mean you must use the automated check-in (of course, the reverse is true).

That is, the FAA is not requiring you to convert your e-ticket to paper before you head for the security checkpoint. Imagine that.