If you look at your list of e-mail addresses, it will let you choose who to share it with if it should be shown on timeline. Previously I had a real e-mail address that was being shared with friends and another real address that was for 'only me'. When I looked at my preferences today, I saw that those settings remained intact and that it added a third @facebook.com address that was being shared with only me.
I think the second field might be brand new. It says either "Shown on timeline" or "Hidden on timeline" and when I looked today it showed both of the email addresses that I had previously set up as hidden and the new facebook.com one as shown. If they would have just marked the e-mail address that I had set up to be shared with friends as "shown" and added the @facebook.com address as "shown", I (and suspect many others) would be happy and it would still allow them to emphasize that people can use @facebook.com e-mail addresses. (Some people might not like this for spam reasons, but I think this is would be far less evil than what they did.)
Also, since they don't share e-mail addresses via the social graph or have other ways of viewing data, what is the point of differentiating 'show on timeline' with specifying who you share it with? None of the other fields (phone number, IM screen name, address etc.) include this "show on timeline field" but rather set visibility based on the sharing settings. It seems like the "show on timeline" field is completely unnecessary and was only added to get the effect that we're all talking about. (So this was clearly evilness rather than incompetence; for some preference system changes one could argue that it was necessary to 'break' old preferences since the new ones were so different, but that isn't the case here.)