I started using MakeMKV when I began ripping my DVDs for Plex.
The program is cumbersome and confusing, and the resulting files are much larger than MP4.
I recently started using Handbrake and now have files that are about 1/4th the size of the MKVs.
I will probably go back and re-rip the ISO images I originally ripped with MakeMKV, but using Handbrake.
Why do people bother with MKVs since the files are so much bigger?
See Otto’s answer in your other thread.
MP4 files will only be smaller if you e.g. use Handbrake to create an optimized version. This version will usually have a lower-bitrate video / audio as it applies additional compression. Experts are capable to create smaller files with Handbrake where you’ll barely notice a difference… though you won’t get that with the default presets.
Also, mp4 has restrictions with regards to what formats the files can contain. You can e.g. not place DTS audio tracks in your mp4 – the same goes for image-based subtitle formats like Vobsub or PGS.
MKV is more flexible when it comes to that. Many use e.g. MakeMKV to create a 1:1 copy of the video/audio from their discs (remuxing the content instead of re-encoding/transcoding it). The files are bigger but this way you keep the original quality.
If you’re using clients that are capable to deal with the higher-quality content or if you have a sufficiently powerful server / internet upload, you should be ok with the “raw” video.
If you feel your files are getting out of hand (too big) – you don’t need to re-rip your discs… just feed Handbrake the MKV files created by MakeMKV.
Keep in mind that Handbrake will at best burn image-based subtitles from a DVD into the video stream; if you want to keep your soft subtitles you’ll need to extract/convert those separately to SRT).
MKV and MP4 are only containers, the size depends more on the codec and bitrate you use.
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