HI,
I was looking at this again myself just yesterday while I was posting here.
My own iPhones (I have two) have one Apple ID each.
One is linked to Messages App on the Mac and that particular iPhone Number.
However on both of the iPhones when I look in Settings > Messages > Send and receive the actual number for that iPhone is Greyed out.
Today nearly 24 hours later after I had tried to set one phone Number and removed the Apple ID to see if the number would pop up as dark text I received one of the Messages Alert text to say it wanted to add the second Phone Number and the Apple ID from the Messages app and other iPhone.
On Checking my second phone I find that the 1st Phones number is now an Alternative as well as the 1st phone's Apple ID although neither are ticked.
ALSO the iPhone Number itself is now ticked.
Messages is now showing both Apple IDs and both iPhone Numbers (Something I was trying to Avoid) although the second phones detail's are not active.
So...
It seems that the OS X 10.8.2 and iOS 6.0.1 combo does isolate the iPhone Number.
I did the Mac first (which also updates Messages to version 7.0.1) and the the iOS devices.
I did remove the Apple ID on one iPhone and this iPhone now has it's Number ticked (even though it is still greyed out).
The Notification on the Mac should not have happened in my book (Different iPhone Number and Different Apple ID.
NOTE.
When you do remove the listed Apple ID you get a message warning showing up that says iMessages anywhere will not be able to use the Apple ID
This does not appear to be true as I also removed the 1st phones Apple ID from the list on the second iPhone and the 1st is still listing it and accepting calls (as is the Mac)

8:09 PM Monday; November 26, 2012
Please, if posting Logs, do not post any Log info after the line "Binary Images for iChat"
iMac 2.5Ghz 5i 2011 (Mountain Lion 10.8.2)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad
"Limit the Logs to the Bits above Binary Images." No, Seriously