Quartersawn lumber is usually chosen for its stability, although it does have a grain orientation that some prefer for appearance's sake. However, most exotic hardwoods are inherently stable, so there's no mechanical advantage to any particular reduction cut. Plus, Warmoth's "modern" neck construction is remarkably stable regardless of cut, so there's no need for the slightly more wasteful quartersawn cut. The added handling and increased waste has an effect on cost, so you have to want it more than flat or rift sawn.
As for sustainability, Warmoth is a fairly small company in a fairly small industry as far as wood use is concerned, particularly exotic hardwoods. Worrying about their effect on the consumption of hardwoods is kinda like worrying about water waste if you spit a bug out of your mouth. All necks are made from hardwoods, which are usually pretty slow-growing trees, so it's easy to use them up faster than they can be replaced. But, you'd be hard-pressed to find many companies making necks out of the hardwoods Warmoth uses, so again we're talking about a small fraction of a small fraction of consumers, which is nothing to worry about. More hardwood trees will die on their own than Warmoth uses in a year by probably several orders of magnitude. If you wanna worry about waste, worry about the millions of acres of exotic hardwoods some countries burn down every year because using the wood has become illegal and effectively worthless thanks to overzealous environmentalists, not the three and half trees Warmoth uses.
Along similar lines, the one piece vs. two piece neck construction has more to do with the efficiency of using a smaller amount of a harder, denser, less available wood for the the fretboard vs. neck meat for wearability's sake than any tonal characteristics.