Ernie, I believe you're misunderstanding.
In the case of people who are moving their emails with rules, Smart Mailboxes can provide a possible solution.
HOWEVER... in the case of the situation Robert and I are describing, Smart Mailboxes don't help, because we don't want the receiving Inbox to determine the From address.
Example: My university assigned me an alias email address: student@example.edu. This address is only a forwarder; it forwards directly to my primary (work) address: workemail@example.com.
So when Mail checks my email, it receives all my email from BOTH addresses at the same time from the same server, and puts them both in the same Inbox. I don't have any rules applied to move the messages, so they both go directly to my work Inbox.
Before Mountain Lion, Mail was smart enough to realize that I want to reply to my student emails from my student account and my work emails from my work account. Now, it just assumes I want them all to reply from my work account, because they are all received at the work Inbox. That is NOT what I want.