Some clarifications about Messages.app in Mountain Lion
There are several things going on here. First, and easiest, Bonjour just appears as an option that you can configure if you have a Bonjour account. No need to worry about that.

As for iMessage, you can have more then one email address that other iMessage users can message you at. For example, when I open Messages settings I have a few different accounts in there. Bonjour is disabled, and two Google Talk accounts which I have disabled also. When I click on my "iMessage" account, my iPhone number as well as several email accounts which are linked to my Apple ID show in there. So I have my Gmail (which I use for my Apple ID), my @iCloud.com and @me.com email accounts, as well as two others that I have arbitrarily added in so that other users can text those emails as well.

Messages.app on Mountain Lion can manage multiple types of instant message at one time. For example, I can have a Jabber account, Google Talk account, and my iMessage account all tied into Messages. When someone "pings" any of those accounts, Messages "handles" that and I can reply.