Overquilt – hydrophobic down or synthetic fill and which shell material?

If you go with a single layer of 2.5 or so Climashield, which is reputed to be about a 50 degree quilt on its own, I think that you get more warmth for the same weight than with down, due to the fact that a down quilt with such a small amount of fill would either have lots of sewn-thu seams, lowering the average insulation value, or have the added weight of baffles, and rather closely spaced baffles to control that thin layer of down. The climashield needs no quilting and thus is a nice consistent layer of insulation. But if you go to the next level with another layer of Climashield, or just a thicker single layer, then the down starts to get ahead. I just made an overquilt with inner and outer of Argon and one layer 2.5 clima, but haven't had a chance to try it out yet. I would go with the lightest and most breathable fabric you can find, and not concern myself with water repellency. Keeping water out from the exterior is a lower priority in my opinion than letting as much moisture as possible escape from the inside.
One thing to keep in mind is that if you size your quilt to really be an effective overquilt, it will be somewhat bigger than what you really need for standalone use, while if you size it for standalone use then you will be compressing the loft of your inner bag and/or not getting full coverage when using it as an overquilt.

I got a 50d EE Egnima about 18 months ago for those reasons in particular. I have used it both is mild weather hiking and to supplement my -5d bag in the winter.

At 10/11oz it's pretty light, & the Downtek is a nice "piece of mind" feature, although I treat it just like any of my down garments.

While I believe everything Paul said is probably true, and is great advice, I have always personally valued the vapor permeability of down over synthetic in any situation. Even at home, our spring/summer down comforter has always been far more comfortable than any thin synthetic comforter/blanket we have tried. I believe this is due to the overall "breathability" of down.

I must admit, if I were to use a synthetic quilt, I'd probably wouldn't think of it as "fragile" as I do with a down quilt. Depending on your use, that could be an important consideration.

I think Paul's advice is pretty solid, particularly the sizing comments

with a majority of the water vapor most likely ending up in the outer quilt, synthetic sure makes a lot of sense