jephyork said:

So I guess at this point my question boils down to: how do I inverse-telecine a video with broken cadences?

Sorry for the delayed response.

Easy on PC if there are only a few breaks as you say, but I have no idea for Mac.

Now, I'm pretty sure that the only "variable rate" in this clip is the end credits, which are natively at 29.97, and wouldn't have IVTC'ed the same way as the episode itself. And I'm going to ditch the credits anyway [...]

Can't you tell Handbrake to only process the main portion of the video, chopping off the credits as preprocessing?