The automatic transcript was fairly poor quality but had fairly precise timestamps. The manual transcript lacked timestamps but was high quality. So I used an approximate matching algorithm to combine them and produce a clickable version of the manual transcript where every group of words was a direct link to that portion of the youtube video. It all worked out surprisingly well. (The other piece was that I hand-inserted annotations to produce an index of various topics and concepts that I thought were significant.)
I don't know how common of a situation this is, since it requires having a high-fidelity human-created transcript. I could clean up the tools and release them, I suppose. I did this for a birthday present.
(I don't have a demo because it's a private video, sadly, and I have rights to neither the video nor the manual transcript.)