This thread is bringing me back some memories!
Yes, you need to do the distinction between each membrane in the rig because they’re independent of each other anatomically-wise. When the wings fold for example, the membranes of a same wing overlap on top of each other and you have no way of doing that if you have only a single membrane where all the feathers would sit. Even when flying, you can find some references showing how sometimes the feathers of one membrane break/split from another.
Here for example, see how on his right wing (screen left) the secondaries have a different orientation from the primaries & scapulars.
Make sure that it’s easy in the rig to bend a whole group of feathers somehow, you’ll need it both in fly and to achieve a good wing closed pose.
With a membrane surface, it’s just a matter of providing a few controllers chain along the feather direction.
On a same note, you’ll need to find a way to easily roll/twist a bunch of feathers with a gradient depending on the position of the feathers—on the photo above for example, the feathers located on the outer side of the primaries are more twisted than the ones on the inner side.
Here again, and as I said before, it can be done using the U, V coordinates of a membrane surface and applying an interpolated value depending on the U (or V) location of each feather.
The drawbacks with adding so many levels of control is that it can quickly create collisions between feathers and I don’t know any magic trick for that so it’s good to add a finer level of control over each feather for “debugging” purposes. Daniele Niero contributed a while back to develop a nice system without collisions for Legend of the Guardians but I believe it wouldn’t work with twist & roll? Maybe he’ll correct me if he passes by here
Here’s the link to his article: http://danieleniero.com/wp/2013/10/12/membranae-deformer/
Last note, and as emphasized by Daniele, make sure that the feathers are not deformed by the surface like a wrap would do, but that they slide instead to preserve their shape.
Maybe I’ll post a rig one day on my blog.
Anyways, I hope it helps somehow!