To be honest I never heard the Plex Team Member saying that Plex Inc doesn't support containers.
The problem is not Plex Media Server. The problem in my situation is the Linuxserver.io container for some reason that container is not working correctly on my server resulting in not be able playing AMZN WEB-DL. I then tried the official Plex Inc container, and now everything is working fine.
I had set my transcode directory to the memory as Jonp suggested. Resulting in the following error in the log:
Apr 22, 2018 14:01:21.267 [0x149a6d9fa700] DEBUG - [Universal] Using local file path instead of URL: /tv-series/Blindspot/Season 3/Blindspot.S03E18.1080p.AMZN.WEB-DL.DD5.1.H.264-NTb.mkv
Apr 22, 2018 14:01:21.270 [0x149a6d9fa700] DEBUG - Job running: EAE_ROOT='/tmp/pms-a5565b46-af26-47c5-969a-2b7d3001353b/EasyAudioEncoder' FFMPEG_EXTERNAL_LIBS='/config/Library/Application\ Support/Plex\ Media\ Server/Codecs/7814ac9-1285-linux-ubuntu-x86_64/' XDG_CACHE_HOME='/config/Library/Application Support/Plex Media Server/Cache/' XDG_DATA_HOME='/usr/lib/plexmediaserver/Resources/' X_PLEX_TOKEN='xxxxxxxxxxxxxxxxxxxx' '/usr/lib/plexmediaserver/Plex Transcoder' '-codec:0' 'h264' '-codec:1' 'eac3_eae' '-eae_prefix:1' 'l2ndpct267ryayw07j9ymhuz_' '-ss' '0' '-noaccurate_seek' '-i' '/tv-series/Blindspot/Season 3/Blindspot.S03E18.1080p.AMZN.WEB-DL.DD5.1.H.264-NTb.mkv' '-filter_complex' '[0:1] aresample=async=1:ocl='\''stereo'\'':osr=48000[0]' '-map' '0:0' '-codec:0' 'copy' '-map' '[0]' '-metadata:s:1' 'language=eng' '-codec:1' 'aac' '-b:1' '256k' '-f' 'dash' '-min_seg_duration' '5000000' '-skip_to_segment' '1' '-time_delta' '0.0625' '-manifest_name' 'http://127.0.0.1:32400/video/:/transcode/session/l2ndpct267ryayw07j9ymhuz/664ffe5b-af62-46de-8316-72376c754009/manifest' '-avoid_negative_ts' 'disabled' '-map_metadata' '-1' '-map_chapters' '-1' 'dash' '-start_at_zero' '-copyts' '-vsync' 'cfr' '-y' '-nostats' '-loglevel' 'quiet' '-loglevel_plex' 'error' '-progressurl' 'http://127.0.0.1:32400/video/:/transcode/session/l2ndpct267ryayw07j9ymhuz/664ffe5b-af62-46de-8316-72376c754009/progress'
Apr 22, 2018 14:01:21.271 [0x149a6d9fa700] DEBUG - Jobs: Starting child process with pid 411
Apr 22, 2018 14:01:21.273 [0x149a737ff700] DEBUG - Jobs: '/config/Library/Application Support/Plex Media Server/Codecs/EasyAudioEncoder-141-linux-ubuntu-x86_64/EasyAudioEncoder/EasyAudioEncoder' exit code for process 410 is 13 (failure)
The Plex Team member thought it was some kind of owner/permission problem.
I then set the directory to my cache drive, but that didn't solve the problem. I played a bit with owners and permissions, but that didn't help either. So I ended up in trying a different Docker container. As you already know that solved the problem for me.