Having hit those first two pain points, I changed my transcode config to 1) run every time, and 2) use a custom bash script as the transcode command. The bash script keeps a plaintext list of files + their modtime and disk size, then only transcodes files it hasn’t seen before. Because it’s a plaintext list and relatively small, there’s not a terrible performance hit since it’s paged into memory.

Not at all saying this to dismiss your criticism though; absolutely would be great to have better OOTB options. Just putting it out for anyone who wants a workaround :).