So yes Ffmpeg no more works with mkv or mp4 hls 
The good new is that now both Mx and VLC mostly properly handle the ts hls produced by Jellyfin simplify handling. (hls is necessary to allow seeking from an external video app). (Mx does not support it with HW profile no image but works with SW and HW+ so I’ll go with it.
As a workaround until next version you can use VLC and select it as a player in settings, this will not use hls so won’t allow seeking but will properly transcode.