I decided to try out Dreamhost’s server-side spam filtering (by MailChannels) since your script Apple Mail - Rescue Good Messages can rescue all of MailChannels’ false positives.
The good news: The script is working perfectly!
The bad news: Mail’s inbox rules don’t get applied to the rescued messages.
Sure, I can select the messages and tell Mail to “apply rules”, but I’m hoping to automate the process. The script is rescuing about 20 retail newsletters (not spam to me, I signed up for 'em) a day. For comparison, I typically get 2–5 spam emails a day (and I’m not even sure how many of those MailChannels is correctly identifying; one motivation for my experiment was to help MailChannels identify the real spam).
It occurs to me that I could create an Apple Script to apply rules to messages in my inbox, but this seems like a bad idea if I can’t make it apply only to rescued messages as they are being moved into the inbox. (My scripting ability is rudimentary at best.)
I’ll probably end up disabling Dreamhost/MailChannels filtering on my domain (my standard practice since forever), but if there’s a smart workaround, please let me know!