I don’t have a solution for you, but I will be watching this thread. Currently, I use Sonarr for library organization, but it doesn’t always work well with anime due to title differences and differences between how seasons/specials are numbered in different databases. So, Shoko was on my radar to try out at some point since it uses anidb.
I use Sonarr, but it does mess up sometimes for shows even when you mark it as an anime to use absolute numbering. It most often happens with older shows that have lots of OVAs that are sometimes listed as episodes and sometimes listed as specials, depending on the database. So, if you are having Sonarr manage your downloads, then it can grab the wrong episode if its database (I think TVDB) and the release (usually using MAL numbering) disagree.