[TpmKranz]

I'm just wondering... What is the benefit of having .mks files instead .srt files?

Subtitles would have to be properly tagged with the correct language, with .srt file you simply add the language suffix.
Standalone subtitle files can be edited easily. With .mks you need MKVtoolnix to export/import a new version.
.mks files need extra functionality to be able to process them, a .srt file is ready to go.

Or is it that you simply have matching .mkv/.mka/.mks file extensions..?

The main benefit would be font attachments. I've only recently started looking into fansubs, but as far as I can tell, these heavily rely on certain fonts being available to either mimic the style of the picture-based original subs or just for the heck of it. One could of course just extract the text-based subtitles from the mks and Kodi will do its best to render them with the fonts available, but that is bound to look way different from the author's intent. I guess if one dropped the attached fonts in the right place, it would look perfect, but that's a bit more involved than just browsing for the mks subtitles and being done.