Harmy said:
Also, I was wondering, would there be any technical disadvantage to making the container of the smaller cropped version mp4 instead of mkv?
See my last. While MP4 certainly isn't limited to Apple devices, they do not play well with sliced video. For maximum compatibility I'd recommend disabling slices for an MP4. They're only needed for Blu-ray compatibility anyway.
Edited to add: Also, MP4 is more limited in the subtitle formats it supports and DTS isn't a thing.