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The answer is... 3. :)

There doesn't seem to be a way to process emails from a mailbox using a mail rule.

This could be done in Applescript.

However, even if mail was processing as a rule, it wouldn't have the original message link that you are looking for.

For me, the answer is,
create an IMAP mailbox that I can move messages to from the inbox using the iPhone. (I call mine: Hold For Later)

Then when I process my Mail inbox on my desktop, use the keyboard shortcut to clip the mail message. I set mine to:

This makes more sense for me as not all the messages in the Hold For Later mailbox I want to have automagically appear in OmniFocus.