My responses are in BOLD. I hope this clears some stuff up!
The one thing I have learned after seeing as many installs as I have is that this stuff isn't wired the same way, even by people in one company. We all learn a different way and it may make sense at the time, but that doesn't make it right. I worked with a guy whose mantra was "They sell the dream, I make it happen". Well, that's great, but he couldn't determine a speaker load with two or more drivers if his life depended on it. He was good at pointing out what someone did wrong after someone pointed it out to him, though. He made more noise than a bad bearing on a high speed motor. We went to the same CEDIA installer test review session and after snoozing a bit and making all kinds of comments about how he knew all of the material in the 5 hour review, I was done and had checked my answers 3 times when I walked out 45 minutes after the start and he used the whole 3 hours. He was exhausted when he showed up after that.
RE: the OP's house wiring- it sounds like the installers did it OK and I don't even really care if they labeled all of the wires since it's easy enough to tone them out. What I really hate is when they use a variety of types for one purpose or use all one color for all of the Cat5e.