Of course messages go to all your devices, how would the notification system know if you had seen it already on a companion device? This is exactly how Calendar reminders worked before messages appeared. I'm not sure how the author would propose using your telephone number on your computer either, considering it's paired exclusively with the mobile phone operator.

Apple are aware of both your telephone number and your Apple ID being used for iMessage. By switching iMessages on, Apple are told to deliver messages sent to your number via iMessage instead of a network text (SMS). Apple demonstrate they know this when you go to send a message to someone and the 'send' button turns from green to blue, indicating iMessage is active on the receivers phone.

Whilst I don't know for sure, I assume this will be the method used to redirect messages sent to an iMessage registered phone number to an Apple ID running on OS X/other iOS devices.

Those are all technical reasons. None of it matters to end users. Apple has, in large part, arrived at where they are today by not concerning end users with why something will or won't work. "It just works" is practically their mantra.

I have to agree with the author here. If you can't get it right, don't do it at all.