MakeMKV is not the tool for this. You need something to re-encode the video if you want subtitles to be burn into it.
Go to handbrake.fr and download handbrake, which will allow you to re-encode the video, optionally adding the subtitles into the video.
Adding Subtitles to my video
Re: Adding Subtitles to my video
MakeMKV Frequently Asked Questions
FAQ about BETA and PERMANENT keys.
How to aid in finding the answer to your problem: Activating Debug Logging
FAQ about BETA and PERMANENT keys.
How to aid in finding the answer to your problem: Activating Debug Logging