I finally visited a good friend of mine who purchased an urban loft and had the opportunity to lay out a built in system. I tried to intervene on his component selections while they were building out but I didn't get very far, actually I didn't get anywhere. He went with in walls for all of his surround speakers, a 6.1 system, with all components hidden in a closet on RF remote. I haven't had a chance to compare how my system sounds ever, but this made me thankful.
In short, the audio overall was painful. The front surround stage with built ins ends up very separate, dialogue does not seem to emanate from the TV screen, and the LR and center do not develop any cohesiveness. The really bad part was all the rear stage is mounted directly overhead. When rear stuff kicked in you wanted to look above you all the time and the sound never melded with what was coming from the front. The lack of concerted sound is both speaker positioning and leveling channels, but with in walls and a lower end Denon AVR with no automated setup, there is not much to be done. I would strongly recommend against in wall speakers to anyone without some serious professional guidance.
That said, I can't say enough about the Audyssey XT function and the Artison LCR speakers I got instead of built ins. The sound stage on my system is just seamless, you sit there and rather than look around the room at where sound is coming from, you simply sense that sound is moving around you while the front and rear come together seamlessly to form a large stage just in front of the listening position, easily tossing sound left, right, and diagonally. Nevermind the crucial difference a potent sub makes.
I guess I just wanted to say that a clean install can be accomplished without in walls, and don't underestimate the power of a great EQ leveling system like Audyssey. With so many channels and speakers we have nowadays, I think it is far more critical to think these issues out when laying out your system, especially when they are fairly permanent with the smaller spaces (and pre-wirings) that us urban folk are dealing with nowadays. By the time my friend was done paying people to pre-wire and install, he paid as much as I did and doesn't have one half the sound quality. Sad.