Hi,
I have since managed to test this myself after I had seen it it in another post.
Like You I got this Messages that the Number was being treated as an Email and "Verification email had been Sent" but it just stays greyed out.
I have two iPhones (G3S) and had lined one Apple ID as an Additional Email on the other.
When I updated to iOS 6 (Having done OS X 10.8.2 first) I was asked by both Phones if I wanted to link the Numbers in Messages (i.e. for each phone the same alert pop up appeared asking to accept linking or the Apple ID's and iPhone Numbers whilst I was in Messages on the Mac).
I declined linking the second Number this way.
In trying to "unlink" one of the additional emails on one Phone I got a warning to say it would be removed from All devices.
I have yet to see if you can delete one name then re-add it to the devices (or app) you want to use it On.

8:40 PM Sunday; September 23, 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 and iPad
"Limit the Logs to the Bits above Binary Images." No, Seriously