User security and privacy is ever-present in Apple's mind so it comes as no surprise that the upcoming versions of iOS 9 and OS X El Capitan are going to feature stronger two-factor authentication procedures to ensure improved security.
As with previous methods, any device that you sign into using two-factor authentication in iOS 9 or El Capitan becomes a trusted device that can be used to verify identify when signing into other devices or services linked to an Apple ID.
According to the release notes, customers who use two-factor authentication with older devices may be required to use a six-digit verification code at the end of a password instead of in a dedicated verification field.
If you enable two-factor authentication, iTunes purchases on Mac and Windows will require you to append a 6-digit code to the end of your password on every purchase. The 6-digit code will automatically be sent to your iOS 9 or OS X El Capitan devices.
Apple does not recommend that customers using two-step verification swap over to two-factor authentication until the feature is available to all.