How difficult would it be to add a workaround in emphatic that multiple lines with the same timing info should be appended and treated as a single line? Or is it so rare that I should just fix the lyrics for this one song and shut up?

Pretty rare occurrence there. If those lines are really that fast, and you REALLY wanted them separate, you could add milliseconds to the timestamps, and the *next* version of emphatic will support milliseconds. That'd be a manual process though, unless someone writes that mystical GUI program that we all want.

Incidentally, since emphatic uses a sorted linked list with unique keys to store the lyrics, the second line (and all subsequent lines) with the same timestamp will just be ignored.