I'm not an expert, and have no experience with the bags and quilts you describe, but here are my thoughts after checking websites for some of the bags/quilts you describe, and also based on my experience from researching and then buying the quilt I've been using exclusively for the past 8 or 9 years (Nunatak Arc Alpinist) --
Re your first question: "1. What is the difference or why is there such a drastic difference in WM and Feathered Friends loft for a 10 degree sleeping bag (~6 inch) in comparison to Enlightened Equipment and Z-Packs Quilts (~3.25 inches)?"
Maybe the difference in loft is because quilt manufacturers measure "loft" based on the quilt laid flat (with loft determined by the height of the baffle connecting the inside lining with the outer shell), while sleeping bag manufacturers measure "loft" from the ground up to the height of the puffed-up bag as it lays on the ground all zipped up so that their claimed "loft" reflects twice the baffle height.
If that's the explanation for the difference in loft described/claimed for quilts versus bags, the sleeping bag manufacturer would appear to be claiming about double the height of the baffles connecting the inner lining to the outer lining of the bag as the "loft" of the bag, even though about half of that "loft" would be flattened when you get into the bag. By comparison, it does appear that quilt manufacturers described "loft" that will actually occur as you lay under the quilt.
The height of the baffle would sure seem to be a pretty important consideration for comparing bags and quilts since the height of baffles (which limit loft to a degree regardless of the nature of the shell material and the quality/quantity of down) are a true indicator of the amount of loft that can be provided by the down that's actually covering you (rather than the down that's crushed flat underneath you).
Re your second and third questions about a cuben quilt vs a "new down" quilt vs a "good old 850/900" down quilt -- I like that "good old" stuff because it's good and it's likely a lot less expensive than cuben or the newer stuff, plus it seems like a cuben quilt wouldn't breath, pretty quickly leaving you with wet down.
Re your fourth question about any other quilt manufacturer to check out, you might look at the quilts at the Nunatak website --
Nunatak quilts are expensive but very well made, and you can customize to fit your needs, e.g., length, fill weight, baffel height, differential cut.