I said in the round one of this comparison that I'd let you know if I got any useful answers to my query on the lilypond list. One of the list contributors got interested in the problem and wrote me a new layout block that does indeed look a lot more like what Petrucci does. You can read the gory details on the list.
Here's the first page of the Petrucci facsimile of Adieu mes amours by Josquin:
And here's the cantus part lilypond produces now that I have the new layout block:
And here's the tenor part from lilypond with the new layout block: