As the maintenance step: In Settings - Server - Scheduled Tasks , is Optimize database every week enabled?
Since no log files have been presented here to verify what is happening, everything stated is therefore assumption until there is evidence.
I do not know what is implied with “distributed transcoding” but the Plex architecture scales no differently on Linux than it does Windows.
I recognize there are outstanding issues. Engineering hours to correct those issues are finite.
Counting all the media in my library, of movies, music, and dvr recordings, yield 49,119 files. All are named by automation to be 100% Plex-recommended naming format and structure. Should I reset the library to zero and begin again, within 8 hours (overnight), all files will have been indexed and properly entered into the database, with artwork retrieved. All this over a 24 Mbps (G.bond ADSL2+) internet service. Upon database rebuild completion, I then query the database for unmatched items. If there are any, that’s a problem. I know this to be true because as part of my QA duties, I frequently build “from scratch” to verify there are no regressions.
How large is your library ?