On the bug report front –
The 1080p encode seems to be missing a framerate in the H264 file. This works fine in the MKV, but if you try to demux/remux, you may have to manually set the framerate or you could get issues.
The 2160p encode has no black bars – not a problem for most people, but it does cause problems when using PGS subtitles. PGS subtitles generally need a 16x9 frame or weird and bad stuff can happen during playback.