This document is difficult to understand for me because I'm a total stranger to the theory of signals and electric currents. What it seems to say is that plugging a balanced cable to two "balanced" ends doesn't guarantee that the signal will be noise-free. This document was first written in 1985 though, maybe things have changed a bit since then.
Physics hasn't changed in quite a few years. The document is fine today too.
Versatility would be one of the most important criteria for me, and not being able to use any other application than iTunes is an eliminatory drawback of Apple's solutions.
Playing and controlling playback from a mobile device sounds fancy indeed, but it is not an exclusivity to Apple's AirPlay; foobar2000 has components providing remote-control and UPnP features, and there are apps for Android that can take advantage of these features.
A/V receivers are not a solution I want to consider at the moment: first they are more expensive, which means that at a given price, an A/V receiver will have either worse sound or less features - or both - than a stereo amp. Second, sending an undecoded signal to the A/V receiver will necessarily cause some problems when the audio track won't be encoded in a format that the A/V receiver recognizes. I fear it will involve perpetual tweaking, like having to convert everything to PCM on the fly from the laptop, and I'll be increasing the already endless list of threads titled "My digital output doesn't produce any sound"...
Sounds like you have your mind pretty well made up, so there's no point in my explaining the advantages in value and technology of an AVR, except to say that except for the really low end, today's AVRs have no decoding issues, no need for tweaking, and no need for PCM only. There are lots of serious technical advantages, but if you're locked into a two channel amp, I won't take the time to explain them.
The same is true on the iTunes/foobar issue.
So, we're back to what to do about balanced wires. All I can do now is reiterate. Just using balanced cables doesn't get you a balanced interconnect, and has no better noise immunity than unbalanced cable. To implement a high noise immunity balanced interconnect you have to have a balanced source and a balanced destination. The destination must have high common-mode rejection (don't bother searching for specs, they are hardly ever there, but that's the critical figure of merit). If you can't find a balanced output DAC, you'll have to use an external device to create a balanced output. Your amp has to have a balanced input, or a device in front of it that has one and converts to unbalanced. The cost of these devices ranges from $50 at each end on up to $1000 at each end.
There are a lot of balanced output DACs, but you'll have to either look at the high end of consumer audio or look at professional devices. For amps, the ones with balanced inputs are clustered in the high-end market, so you'll pretty much need a conversion device or pay up.
Let me offer one final reality check, which you can pick and choose from if you wish. The devices that make the biggest changes in sound quality are, in descending order of impact:
Speakers (huge, quality is everything here)
Number of speakers and channels (huge, everyone can hear the difference every time you double the channel count)
Speaker placement (significant. Bad placement will undermine everything else on the list.)
Room treatment (can be very significant, depends on the room. A bit of treatment in the right place is a very audible improvement.)
Calibration systems (Audyssey, Pioneer MCACC, Yamaha YPAO, etc.) (particularly significant if you can't optimize the above two. And any cal system beats none, even with treatment.)
Audio file formats, bit rates, etc. (this one could be bumped up the list, but it's assumed you're already at FLAC, but once you're at high enough quality it doesn't matter anymore)
Play software, amplifiers and AVRs, DACS (negligible, imperceptible)
Exotic wire types and power conditioning (no difference at all except in very extreme circumstances)
Might have missed something, but it's probably not significant.