I always interpreted that to be regarding the inputs on the Three if no Control is connected. In which case AES is preferable to analog, and if AES is not available it can be converted from SPDIF with an adapter.
Actually no, I've never tried that input - I had assumed that it would be the same as spdif so didn't bother. Where did you read that the AES input is preferred? I can't see anything about that in the manual.
The iso-200 looks like a nice fit, judging by your photo. I opted for the pucks as I wasn't certain if the iso-200 would fit correctly - but it looks like either would do the job just fine.
I don't doubt that the kiis may perform better on seperate stands - however I use a sit/stand desk and having them on the desk allows me to maintain an on-axis listening position regardless of whether I am working standing or sitting. It makes mixing a rather pleasant experience!
They are the standard size ISO-Pucks. They do make a subtle tonal improvement. What I didn't expect, though, is that they are actually incredibly stable. They are like little suction cups that stick your monitors to your desk.
I recently got a pair of Kiis for studio work/composing. Very analytical and excellent bass extension - perfect for mixing. They are a pleasure to work on, but it is their size that makes them truly impressive. They easily fit on my desk with all my other junk!