MKV:

ffmpeg -i input.mp4 -f srt -i input.srt -map 0:0 -map 0:1 -map 1:0 -c:v copy -c:a copy -c:s srt -metadata:s:s:0 language=id output.mkv

MP4:

ffmpeg -i input.mp4 -f srt -i input.srt -map 0:0 -map 0:1 -map 1:0 -c:v copy -c:a copy -c:s mov_text -metadata:s:s:0 language=id  output.mp4

Use MKVPropEditGUI to edit MKV

Source : https://www.reck.dk/use-ffmpeg-to-add-subtitles-to-video/