MakeMKV can only make them smaller by removing tracks within the MKV file, and there are better tools for that.
Handbrake is how I make them smaller. For anime from BD, it's typically 80% reduction while maintaining 1080p resolution. "Regular" movies is usually on the order of 40% or more.
Two identical streams for main movie - which to pick?
Re: Two identical streams for main movie - which to pick?
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FAQ about BETA and PERMANENT keys.
How to aid in finding the answer to your problem: Activating Debug Logging
Re: Two identical streams for main movie - which to pick?
Oh wow, awesome! Looks like I have a new movie-ripping process now. 