Kieshi save PT settings for each video separately
But it does, if I set a pt setting and come back later to watch it the pt setting is still there how I left it.
If it's not working for you like that then it could be your data saving options, example on meta...I think if you turn it off, any settings you make to apps won't save, and apps you Uninstall but install again they won't have any settings you previously made.