There are some subtleties… For example, some movies have what are called forced subtitles. For example,
The Hunt for Red October (1990) has the part near the beginning where the Soviet crew is speaking Russian. Even when you're watching the English soundtrack you want the English subtitles to appear during this part. Those subtitles are the forced subtitles.
MakeMKV has undoubtedly included them in your rip, but it is anyone's guess how they're packaged on the disc. There are no standards and every disc seems a bit different. In any case, there's are flags for that track in the metadata of the .mkv file that should be set properly so that Plex can find the forced subtitle track and turn it on automatically. The flags are 'default' and 'forced'. If those are both set to true then Plex will see that and play it properly.
The
mediainfo tool is very helpful for looking at .mkv file metadata.
mkvpropedit (part of the
MKVToolNix tools) is very helpful for updating the metadata of a .mkv file.
Furthermore, I like to name things like commentary audio tracks so they show up in a useful way in Plex.

- tracktitle.jpg (24.38 KiB) Viewed 2415 times
This again is a .mkv file metadata action. You can do it either via naming tracks in MakeMKV before you rip or afterwards using mkvpropedit.