Now I don't go around singing this kind of thing, or any other kind of thing actually, but I do listen to a lot of people who do, and I think that keeping the notation as close as possible to the original when transcribing it has to be a good idea, because if you start thinking in bars and tuplets and so on, it's bound to impact on the performance (mind you, so is learning an unfamiliar notational system). Text underlay is also a recurring problem in this repertoire - for example, what actually happens at the end of "Belle bonne" - a massive extension of the last syllable? some other syllable? an instrumental postlude? (if instruments are indeed appropriate at all) or is the text in the MS not even intended to be lined up with the notes it appears under? etc.

No, of course they're not tuplets, but I'm uncomfortable with the notion that they are best thought of as one-and-a-half times something rather than a sesquialtera-ratio pulse; it's a question of how one conceives of the syncopation.  I guess the only satisfactory solution is to use a different kind of notehead entirely - perhaps in a different color? 

Continuing from the "Handel oratorios" thread, where I opened a can of subtilior worms:

What is Fumeux fume about, asks Reiner. Mary Springfels has this to say: "Solage's "Fumeux fume" pokes fun at a group of giddy young men who called themselves the Society of Fumeurs (smokers). One of their number was the poet Eustace Deschamps, the self-proclaimed nephew of Guillaume de Machaut, and a habitué of the French court. I suspect that he is the "Smokey" of the song. The poem, a rondeau, is unusually short, while the composition is unusually long, inviting the singer and the audience to lose track of what little sense the words make in the first place. The marvelously bizarre chromaticism of the music also leads the musicians through tonal labyrinths. In short, the piece is a vivid, merciless evocation of drug-induced inebriation. Did the Fumeurs smoke? and if so, what? Opium or hashish are the most likely candidates."

This is a pretty fanciful interpretation, it seems to me. And indeed, were these drugs available in northern Europe at the time?

There's an interesting article by Yolanda Plumley (Early Music History 18 (1999), pp287-363) in which the matter of citation and allusion in this repertoire is examined at length, and whole complex networks of quotes and correspondences are revealed, without really tackling the question of why they might be there.

The big error from the get-go is to use the term syncopation, I think. That implies too strongly the sense of weak and strong beats, which is a simpler notion of meter/mensuration/tactus/agogia hierarchy than scholars presume was being practiced. As for your discomfort with something being one-and-a-half times something else, perhaps it's because you have a Latin fetish. sesquialtera means 'one-and-a-half times'. Meanwhile, the 'something [vs.]... something' is reflected in the term ratio.
Meanwhile-meanwhile, putting 4:3 is much worse, as it implies that these are mere numbers, and one could just as well have made it 5:3 or 4:x. This is not possible for this particular notational world -- it required another innovation in another part of the galaxy at another time.
I like your idea of simply making the notes red or something, but don't you think the dots are fine as long as they aren't sung like a syncopation? The danger that the dots will be misunderstood with this caveat is, I think, less than the danger that your red notes will simply make the edition too expensive or unnecessarily cryptic. But perhaps you wanted them green or blue. That's different. :-)

I would generally agree-ish, ... however, it's certainly worth noting that Arabic numerals start figuring rather prominently in several Chantilly MS pieces, referring directly to ratio (and, well, even "pulse streams," as Evan would say).  Somewhere up there on this thread is a link to a Rodericus ballade w/ various 4s, 3s, and 2s scattered about, particularly in the tenor, if I remember correctly.

Edit:  Apparently, that link was posted on another thread entirely, and I can't seem to track it down.  Hm.  Anyhow, here goes:  http://www.aaroncassidy.com/images/scores/rodericus2.gif

Edit²:  only 3's and 2's, no 4's.