OK. But the Plex forum doesn't seem very active. As I can see, you are engaged in a monologue with yourself.
Anyway, I will add the conversion to 30/60 fps globally. It will be available for SBS and T&B also, even if it's not necessary. Nobody is forced to tick that option.
Good luck for your conversion. I have tested it here by encoding first the demo clip to SBS and then converting it to FS 60fps, and it worked fine (but again I can't test it really). It should work for you, but try with a short clip first.