@kieranc Mike already answer the majority of your questions. The only thing I’ll add is this:
MP4 is a good streaming container (well it works).
MKV is a great storage container but a lousy streaming container.
We care about streaming with Plex so that makes MP4 better to us.
You are in full control of what subtitles are kept or thrown out. By default it will rip ENGLISH subtitles (ini setting) out of the MKV and create a seperate .SRT file. So they aren’t lost, just transformed into something more usable.
At present it does not use Quick Sync and I’m not sure it should. Sure it’s faster but still doesn’t match the quality of pure software encodes (very close on the latest GPUs). I personally have a different philosophy when it comes to QS. I WANT IT BAD for real-time encoding but for encodes that are meant to be permanent I want the absolute best I can get for the time it takes to do. With that said I’ll probably add this soon. 
@don.alcombright
Yes you DO WANT relocate_moov = False
I create the moov atom a different way than the original script did. It’s faster and has less issues with compatibility.
Carlo
