Since passthrough is not possible, ask yourself: Do I need to re-encode? If you only want to change the container from MKV to MP4, you usually don't need to encode anything, you just change the "wrapping" around the video. Do I have to re-encode? Couldn't I just swap the container? So, anytime you're changing containers with Handbrake, your video is going to get re-encoded, which means it a) takes time and b) may introduce quality loss. HandBrake is designed to be a video transcoder. Sorry, adding video passthrough is not planned. See also the respective feature request that would have enabled video passthrough:
MKV to MP4 in your case), Handbrake will re-encode the video. When you're using Handbrake to convert from one container format to
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