Granite is just fine to use inside a shower, but as you said, a good sealer will keep it looking good for a while. You can build the niche out of durock and then apply anyone of the liquid membranes that are specified for a shower. I use granite for niche bottoms frequently.
As far as the plumbing goes, I have seen your set up done a few times. where the controls are on one wall and the heads and sprays are on another. I'm not a plumber, so I can't tell you how to do it, just that I've seen it done.
As far as the glass, I ALWAYS
hire a glass company. They do the best work for my customers
Best of luck