And at this point, after having done several "mixed" deinterlaces in Handbrake and being thoroughly unsatisfied with the results (it gets the 30p and 24p content mixed up all the time, or takes too long to recognize the change, or sometimes gets field order mixed up for a few seconds which makes the video looks weird and blocky), I am unfortunately looking into using AviSynth for the DS9/VOY encodes.
It realistically shouldn't be that difficult to use Handbrake as the encoding engine anyways.
It's funny - the first AviSynth result that comes up for deinterlacing mixed frame rate content is actually a plugin called "AnimeIVTC", and it does in fact seem to have a solid hybrid content option. The idea that I might end up using a filter designed for anime on Star Trek amuses me greatly.
Deep Space Nine is my favorite anime.