Once the options were available, I always set....
Video Format: MKV (MKVToolNix)
Video Resolution: Full HD - 1080p
Subtitle Format: Remux into File.
I use it, because it works. As far as I can recall, I've never had an issue with it in StreamFab. Also I've used MKVToolNix for remuxing and other stuff on its own, so I trusted it.
Is using MKVToolNix better than FFmpeg? I can't answer that. I can only share what works for me.