When tsMuxer creates subtitles from SRT files, it has limitations. Usually not very important limitations, but occasionally critical. For example, it's limited to one font for all subtitles. I've found Arial works really well for Latin, Cyrillic, Greek, Arabic and Hebrew, but Thai is way better in Tahoma. And CJK languages all need totally different fonts. Then there's sizes. Thai and Arabic typically use a larger font size than your typical Latin text, because that makes them easier to read. I also do some text alignment business that tsMuxer can't do at all. Then there's the black background on SDH subtitles, repositioning subs for alien dialogue, Japanese subs for ROTJ not even being available in text format yet, and so on...

All of this is, to some degree, my personal preference, but I read up on things and like to think it's a least a somewhat informed preference for how things should look. I'm always going to suggest using the SUP files if it's even remotely possible. The SRT files really only exist for when the SUP files won't work for you.