I'll take my turn here...
1. Don't worry all that much about the body shape or wood, as far as the sound goes. Just get the right pickups for the job, and the right trem or hardtail setup for your needs, and you'll be well on your way as far as the sound goes. Think about the influence of wood like this: neck wood > body wood > fretboard wood > body lam wood. If you're willing to give up on flame maple, you can get most common woods in one-piece tops for very reasonable charges. I've got a one-piece swamp ash telecaster and only paid USD 75 extra for the one-piece aspect.
2. I'll reiterate that they are not a custom shop. You can definitely get exactly what you want though. Just call up PRS or Gibson and have them make it for you to your exact specifications. Once you get the price quote, you'll stop being mad at Warmoth. Don't get mad at the company because they won't make you a USD 10,000 guitar for USD 1500. The reason they won't do all that special stuff is because they only charge, for instance, USD 220 for a paint job. That's the cheapest paint job you can get in the US and so they need to streamline production, make it efficient, to turn a profit. Basically, be reasonable and don't go to Macdonalds demanding filet mignon.
3. As already explained, bookmatching will get you a pretty symmetrical finish on a flat top, but on a carved top it's impossible because the act of 'carving' exposes new wood grain, so you can't know in advance how it's gonna look. Notice that in the showcase, most of the strat bodies have nearly invisible lines, and they're almost all two-piece, that's because on a flat top its relatively easy to match the grain.
4. They have more strats and teles because that's the market. Most of the aftermarket and build-it-yourself is all built around strats and to a lesser extent teles. Warmoth has more body choices than any other similar company that I've seen, and as far as I know they are the only one to offer a body similar to PRS.
5. If you're that worried about the width of a VIP, etc., maybe you shouldn't order a guitar you're never seen - maybe that isn't the right road for you. I'm just saying, there's gonna be a lot of unknowns and you've just got to make the leap or not. Do call up PRS custom shop though and find out how much it would cost to get just what you want. Another thought - make a careful purchase of a nice used PRS on ebay, get the all-rosewood neck, every one I've played has been awesome. I mean, if that's what you really want, that's what you should get, and they are pretty reasonable used (USD 1500 for a McCarty).