WRT increasing dose with volume, per the owners manual (downloadable pdf on the Website) it's linear, i.e. one cycle per liter.
For me, using a larger treatment vessel is simply a workflow consideration. I find it easier and faster to treat larger volumes when collecting a gallon or more water for camp. Strictly personal preference. Likewise, when using a bottle smaller than 1L, the cycle can be halted in less than the standard time. That's what I do on the trail.
There's no reflection mechanism at work with the supplied bottle, directing UV back into the water, so any bottle material is fine. One could use metal or glass, for that matter.
IIUC the maker's warning about soft-sided containers is the lack of physical protection against breakage, not a concern about the material itself. So long as one's not storing and transporting the tube in a Cantene, there's no reason not to use one for treatment.
As to UV radiation, the only potential danger from the AS's emitter would be looking directly at the bare discharge tube. From what I've read, it's a challenge to find materials that are sufficiently transparent to the relevant UV wavelengths from which to make the lamp itself, which is why it's quartz.
I think of the warning as being along the lines of the "Do no operate heavy machinery..." sort. Hopefully, not many folks will sit in camp after dinner, gazing at the pretty blue light.
From my conversations with the AquaStar folks, I'm impressed with their relevant knowledge of the technology and the biology. As I'd expect, there's conservatism designed into the product, both in the light intensity and the treatment cycle time. Given the product's important task, it's what I'd expect.
You and I must certainly hike different parts of the Sierra, but continued good health to you!