So, i found a pretty good workaround. I set up new rules that, instead of moving the messages as they came in, it would simply flag them as gray. I created Smart Mailboxes for each of my accounts, Which only shows emails to the proper account, which have been flagged as gray. I have messages that i flag red for "To Reply", Yellow for "To do TODAY" and Green for "To do" (eventually). I set keyboard shortcuts to quickly flag them for one box or the other. Once they are flagged, they only show up under "Flagged", and no longer show up in the smart mailbox for each email. When i'm done with the email and ready to archive, i use a keyboard shortcut to clear the flag and then move it to an archive folder (I guess you could also just "archive" it)
It's not as simple as I used to have it, but it's a pretty good workaround, and it DOES reply correctly from the right email address. The "inbox" is pretty full of ALL the messages that are still flagged and not archived, but the smart folders for each account will be nice and clean. You should only need to mess with messages in those folders and the flagged ones.
Hope that helps somebody out there 🙂