I think the timestamp is OK, my biggest complaint is the huge amount of whitespace between the rows and the small size of the box. If I designed YouTube I would put the transcript on the left side above the video description, with a button that expands it to full height so there's no separate scrollbar for the transcript anymore, it's just all directly in the page.

BTW when I went to look at a video just now, YouTube actually served me a "Search in Video" box at the top of the transcript. So I guess the feature exists, they just haven't rolled it out to everyone yet.