Most times processing goes good. for me.
Using my main drive nVME SSD and temp folders, etc., on a secondary WD SSD.
WD SSDs are rated at 560 MB/s read/write speeds.
If I could have done several NVMe SSDs, the speed ratings are off the roof for the one I do have.
The final product goes on a pretty darn fast external spinning HD.
So look for faster drives. If you have extensive memory, sadly I only have 32 gig; you can also make a RAM drive for the temp folders for SF. I think it is more likely it would need to be 128 GB of memory.
As for MKV and MP4, I go back and forth between those formats. Also, for MKV, you can use (FFmpeg) or (MKVToolNix).
I am not sure if one is overall faster, but it is worth trying all formats; all formats play fine on my PC and with Plex on my PC to my Roku.