I read this tread with interest and thought i would weigh-in. Technically speaking, there are not really any issues having multiple ATVs in the same house. Each ATV can run independently of the others without conflict with the exception of the remote if they are physically next to each other (why would you do that??), and for AirPlay if they all have the same name (ie all named "AppleTV"). Every ATV is even capable of using the same instance of iTunes at the same time. That I was impressed to find true.
To solve any conflict problems:
Conflicting Remote - simply "pair" each remote to it's own ATV, including if you use a universal remote.
Conflicting Name (only applies when using AirPlay) - simply choose different names for each ATV! There really isn't any conflict, whichever one you choose will play, but you won't know which ATV is the one you're choosing.
If you are having trouble reading from one iTunes instance with multiple ATV at the same time, something else is causing a problem, because technically it works. Probably a network issue, since "out of the box" it should work - if all ATVs on the same network and also using the same home sharing account etc. Both ATV need to be set-up nearly the same except for the name of course.
My biggest challenge has been to get multiple ATVs to play the same thing at the same time, without using a HDMI splitter playing from just one ATV. Since multiple ATVs can play from the same library at the same time, i thought there must be a trick to get them to play the same thing without having to install more wires. Alas, i haven't found any way to do this, except by pressing "Play" on both remotes at the same time (one being a wireless Harmony to start the ATV in the other room)
Here I am talking specifically about playing video from the iTunes library on multiple TVs. On the other hand, it's quite easy to play the same audio on all your ATVs at once. You simply "play" from iTunes app on the computer and choose all the ATVs you want to output to. This can also be accomplished on the mobile "remote" app but NOT if playing from the mobile library itself. Using the iTunes remote app, it actually plays from the computer, just controlling it with the mobile. Mobiles are apparently NOT powerful enough to handle playing to multiple AirPlay devices - not even audio. (actually they can be "forced" to do it with jailbreak but it's not smooth and of course, you have to jailbreak your mobile)
Everything I write here is not expert speculation but actual experience. It would be cool if Apple could add the "synchronized play" feature to the mobile remote app. Seems it should be an easy feature to implement for controlling multiple ATVs at once. I thought someone might have figured out how to "hack" a solution by now, but couldn't find any. Wait and see.