Yes, I know I could extract the video track, transcode it, and merge it back in again. But a large part of MakeMKV's appeal is that it's really easy to use and pretty much turnkey (apart from making me guess which checkboxes I should leave checked, but that's the topic of another thread

It'd suit me fine to have MakeMKV invoke a command line tool to actually do the transcode - in fact I'd prefer to have some control over the parameters used for the transcode.
-- Paul