I also got to visit the site every day and take pictures, which is really nice to have. Especially the day before they did drywall, I went nuts with pictures and now I can tell you exactly what the inside of every single wall looks like, what the electrical looks like, the plumbing, conduit, smurf tubes, etc.
Also, if you are nice and polite, you can talk directly to the subcontractors in some cases and get even more customization at a great price. E.g. the electrical guy offered to run cat5 throughout the house for a few hundred bucks. He couldn't terminate it, because he's not licensed for low voltage, but he could run the wire itself and leave it coiled up in a single gang box in every room. The builder didn't think to offer that, but having a chat with the electrician when he was on site gave us that option.
Stick to buying spec houses. They will always be better than a custom home because people get to examine the house before they agree to buy it. Whole world changes when you are under contract for a build/remodel.