It just doesn't sync properly. If you delete a message on your phone, it will remain on the computer. When all devices are using iCloud, it's nice. You can have the app open on your phone and computer, delete a message or message thread on either and it will instantly vanish from the other device. What I did run into was it frequently didn't sync properly if a device wasn't on or offline. Glitches like that are no doubt one of the (many) reasons why it's not released yet.