Okay, I will just take it in order.
The "recommended" water line placement is just a suggestion. If it fits, it fits, and it will fit or it can be made to fit without opening up the wall.
The CST412MF and 416M are 5" either side of the flange centerline at the base, and taper up from there. There's also an indentation in the back. Most likely, your current hardware will fit just fine. I am assuming that you have a 12" rough-in (12" from the finished floor to the horizontal centerline of your existing flange). However, if your waterlne protrudes too far from the wall in an inconvenient spot, your plumber (or you) can just install the Dahl Skirted Toilet kit (very easy) which incorporates an excellent Dahl quarter-turn valve and a 90-degree bend in one unit.
http://www.dahlvalve.com/products/mini-ball-valves/skirted-toilet-kits.php If you look at the photos at the link, the fact is that that pipe in the photo still protrudes much further than it needs to; you can use the kit so the 90-degree bend occurs right when it comes out of the wall. Your placement is fine.
On the Maris, the spec sheet indicates that it might be a little close, but also might just fit. If not, as I said, you just install the Dahl kit and you'll be fine. There is a roughly-3.5" gap behind the toilet bowl and the wall on a full 12" rough-in, so the Dahl kit would solve the problem.
On the Nexus, it's gonna look fine. These suggestions are mostly dealing with the situation where you're using a hard piece of pipe vertically into the base of the water fill valve on the toilet. Since almost everyone uses a flexible braided hose, it doesn't matter that much where the supply is as long as it is in range. And yours would be fine with the Nexus.
Hubby's concern is a little overly-concerned. It's rare that you're going to damage the china on the bowl or tank such that you need to replace it. They do sell them separately, so indeed you could buy just one of the components. Indeed, the most-often replaced thing is the lid. (Someone opens it and drops it on the stone floor, for example.) The benefit of the two-piece is that you can carry it up the stairs more easily (2 pieces). Its also easier to mold to smaller pieces as opposed to one big one, and hence a two-piece is often a little less expensive. The disadvantage is that the most likely time that you're going to crack the china is when you install the tank of the two-piece and tighten too much (or someone, fearing that, undertightens the tank, leaving it wobbling, whereupon it gets cracked when someone pushes on it). Again, not a frequent occurrance, but not an issue in the one-piece. So if you guys like the appearance of the one-piece, go ahead and get it.
As to flush noise, I am mystified by that reviewer's comment. These are all gravity toilets, which are inherently-quieter than the pressure-assist models. Some people are vastly more sensitive to stuff like the sound of running water than others. All the newer low-flow gravity toilets dump the water into the bowl faster than their predecessors, which would fill up, swirl forever, then go down. These are more like slurp, gurgle, done. Because the Aquia is a washdown flush, maybe there is an almost-imperceptible-to-normal-humans rush of more water down the sides of the bowl than the models in which much of the water runs across the base of the bowl in a siphon jet. Based, however, on my personal experience, it's not a real issue. Here's a video of the Aquia III flush. Note the great bowl wash. Note the absence of any excessively-loud sound, but it does run the water into the bowl a little longer than the original Drake, for example. (Look up CST744S on youtube if you want to see a video of that toilet flushing. Ignore the apparently-loud refill on that toilet; it doesn't really sound like that, which was the result of an oversensitive cellphone microphone.)
Aquia III full flush:
The Aquia does have a little smaller water spot as you point out. I think it's adequate (which is confirmed by the fact that literally more than 99 percent of Terry's customers don't return them and instead buy more of them). And there's always the "courtesy flush" if it's an issue for certain people after an excessively-large meal. And no toilet today will have the swimming pool of water in the bowl that the old toilets did. 'Nuff said.
You're becoming a really-informed consumer about this stuff. The good news is that there is really no "wrong" decision: most of these toilets would be fine choices with which you are likely to be happy. Come back with more questions if you have them.
EDIT: Saw your subsequent post after writing this. You found the dahl thing yourself -- good researcher! Most people can't tell the difference between the 1.6 and the 1.28 and indeed some of the difference is really in how much water is sitting in the bowl. However, it's another third-of-a-gallon of water going through the thing, so maybe it helps clean a little better or something, but it's not going to make a meaningful difference in performance under almost all circumstances. Bottom line, though, is that bowl wash is going to be better in the Aquia than the Nexus, which the video should illustrate.