All of the things Alan stated are facts on just about every large project.
The biggest fact is that if presented with the real costs the client would balk.
That tells me these systems are better suited for the commercial market. Untill reliable modules and equipment are being used in residential systems, labour and programming charges are mearly a number to hopfully recoup some of the costs.
With lower margins of the equipment it really looks like a loosing business model.

Of course thats not true.

If Alan is out there troubleshooting issues that are wire related then someone (not the client) is wasting his time. My tech's have drawings, these outline every detail of how I expect everything to be connected. They MUST also test systems once connected to ensure they work. All networking issues must be resolved (Escient or other items that need an IP etc).
That way the programmer can come in with the bulk of his work done ahead of time and in the perfect world he should only have to work on smaller issues that may come up. There are always other things, but if the back end (installation) was done to your companies specification these other things should be minimal. Not adding 5 more unpaid days onto your programming time.
Equipment should be staged ahead of time, this way you don't find out on site about Sony and any HDMI issues. Not always easy to do, and once again, technical crew should be the ones finding these problems not the $150 hr programmer.

I have spent hours trying to make a multi video system work only to find that the techs' didn't test their custom made cables. And of course it was the first monitor I was working on so I end up spending too long looking at the RS232 codes and ports this or that, checking for Null ect, only in the end to find out it was their cables that were bad. Never again... they come back on their own time to fix stupid issues like this, so now they know, test test test.

This thread keeps going into other aspects of large projects, and I think the main topic was answered a long time ago. If an article is going to be written about being an informed consumer when it comes to programmed automated systems, it should also remind clients to find a dealer they feel very comfortable with, as the dealer or CI will be in their home long after all other trades have left. Plus something about how to be a good customer of a CI firm, it goes both ways.