I wish I could explain but I can't
My collection consists of:
TV->VCR->DVD->Kodi
TV->DVD->Kodi
Bought VCR->DVD->Kodi
Bought DVD->Kodi
TV->TVHeadend->Kodi
Over the years I've used DVDShrink, MakeMKV & Handbrake. Everything goes through Handbrake and the framerate setting is one I've never touched. I just looked and its set at 30fps Peak Framerate
1. SLOW Linux machine
2. Handbrake doesn't contain any mechanism to identify only those with a framerate of 125fps so I'd need to identify and select manually outside of Handbrake