By popular demand, I went ahead and added a new preference screen for the mail utilities. Check out the updated files at the bottom of the article where you can download them. You can now configure what database the mail rules run against. This means you can configure it to run against a mail archive or always be a local replica – regardless of what mail file you opened. The behavior if the fields are blank is the mail file will be used – the last one open.
I also fixed a problem where the icon does not show in Notes 8.5.
You will then see the path for what file is used. If it is a local file then it will look like a file path.