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Nice post. I've also struggled with this because I don't leave a computer running all the time to process emails that I send to be put into OmniFocus.

I've recently started moving emails on the iphone that I want to process to a different IMAP folder. When I process that email account I go through that folder and either process into OF, delete or reference.

My question with your workflow... why can't you process the inbox? Is it because you want to keep all those notes searchable and on the iPhone?

Here's an adaptation:
create an IMAP folder for Send To OmniFocus
create a mail rule that processes all mail items in that folder into OmniFocus and then moves the message to an archive folder.

when on the iphone, move messages into the Send To OmniFocus.
When your Mac Mail application processes those emails in the folder, it will add to OmniFocus and move the message out.