The problem of double notifications has been reported long ago, but has not been addressed and solved yet. If the coming re-introduction of the Email browsing (Make Contact Requests more visible) will also allow deltachat to emit notifications for regular emails again, it could be one solution to turn the notification off in the standard email client, and let deltachat handle that.
Concerning the SIEVE filter, it may be more robust to filter by message IDs, in-reply-to, and references starting with “<Mr.”, to also get the replies to chats sent from classic email clients.
If you get it working, you could add it to the SIEVE part in this wiki page: