It's probably not only iOS/OS X dependant, but they will also need to change something behind the scenes.
As of now, it does in fact seem like messages are being divided (for the recipient) into different discussions/chats/messages/what have you according to a device specific ID (one for the computer, one for the iPhone and so on), and not according to Apple ID or even by contact.
My guess is that with the release of iOS 6 (and 10.8.1), messages sent from no matter which device will be identified by from which Apple ID it's being sent, i.e. being able to merge phone number and e-mail address(es).
But I wonder if it will be possible to exclude for instance messages being sent to one's phone number to arrive at the computer...
Originally Posted by kmj2318
Not until iOS6 is what I keep hearing. Although when Messages was in beta, it integrated my Apple ID with my phone number perfectly, but just after upgrading to Mountain Lion, it no longer works the way it did.
I have the exact same thing. With Messages beta, I got messages sent to my phone number after having entered it in my Apple ID info. Now, nothing.