If indeed the bivy isn't breathable, one issue you might have to deal with is insects, depending on exactly when you're there --- if the bivy isn't a credible place to spend your time then the bugs could impact your mental health (and blood supply ...). I used a single-wall tent through the Sierras in June of last year and didn't encounter too many bugs until towards the end, but in more common backpacking times I understand they can get fierce, and from what I experienced the last few tens of miles it's easy to believe.
Footprint: IMO a really light footprint (GG polycro is a good choice) can be useful if you think you might want to cowboy camp very often, either just for the pleasure of it, or because the bivy is too warm, but I guess you could just sleep on top of the bivy and use it as your ground cloth.
The potential for storms or generally bad weather bothered me for the Sierras too, but with a lighter pack weight and --- you should be in good physical shape by then --- it's not hard to "walk high but sleep low", and not have to camp in areas that seem particular exposed. Poncho plus bivy for me is a combo to use when I either don't expect or know I can reasonably mitigate really bad weather (and bugs).