Hmm.. I think, MPEG4 is better and use less power (CPU). Compress is way faster with a MPEG4 (ffmpeg). There is very slim different with a video quality, you can use higher bitrate for MP4 MPEG4 vs MKV H264 and you get same size. I try this many many times with the Handbrake. H264 If you want many audio or subtitles files in the one file . IF you want to use H264, you must play setting a lot or file size is going to be very big!

Of course you can try, but we do not have that much power to compress video files on the fly