I wonder how much of that is because subtitles themselves are a mess, and it's highly dependent on the environment the player is running in.
Some subtitle formats (notably DVD & Blu-Ray, if you're ripping your own content) are actually image formats with timecodes. There are other text-based subtitle formats. If a player (say, the Apple TV) supports one type but not the other, Plex has no other option but to "burn in" the subtitles on playback.