Issues with Handbrake and PGS subtitles

I'm using handbrake to get MP4s to populate my Plex media server and some of the movies and stuff I have use the PGS subtitle format and it doesn't seem to work properly, instead of having the option of turning subtitles on and off they're just always on and if there are multiple subtitle files it just uses the first. I've had people suggest hitting "burn in" in the settings but that doesn't seem to do anything helpful. So if anyone knows how to fix this I would really appreciate the help, and if there is no good way to fix it any suggestion of a good website to get subtitle files from. thanks in advance.

Try writing it as a MKV and use pass-through instead of burning it into the movie

How do I do that?

HandBrake supports SSA and SRT subtitles. Finding the compatible subtitle formats makes it work.
The popular subtitle downloading sites:
The method to add subtitle with HandBrake: