Why are you using cuben specifically? Water resistance is great for down, but not nearly as beneficial for synthetics (pretty much the main benefit for using synthetics at all).
The cuben strips will not breathe, so they will act as a vapor barrier liner. Essentially your body sweat will be trapped in the insulation anyway using cuben. This is ok for sub-freezing temps, but for a summer quilt it will be miserably hot and sticky for most people.
M50 is supposed to be pretty good with regards to wind protection, yet still breathable so this gives it the edge over cuben. With a quilt drafts will be your biggest issue anyway and material doesn't help with that anyway.
A larger tarp or a tarp/bivy combo will solve any concerns with wind/water exposure and provide added comfort and flexibility.
So basically using cuben probably won't net you much. It'll be more of a pain to work on since you'll have multiple panels, and the extra thread/tape used will probably negate the weight savings of using a .34oz vs .67oz fabric on small panels. Add to that subjective decrease in comfort and I'd say stick with the simple but effective design everyone else uses! I do like using silk for the liner though!