I have not recently bought a new home, but my mother did - a year and a half ago. Yes, you can request that they paint a different color, but expect them to charge you if its not one of their standard colors (usually not much... negotiate the cost with them if it seems high). And yes, you can request an additional keypad on the second floor, but again, you will have to pay for the wiring and the pad.
Also, if there are other upgrades that you want, ask to see if there are any packages that would include the requests you are making. You might find it is cheaper and you get more if you go with a package.
Do visit the build site often during the building phase. Not only can you see how it's going (everyone makes honest mistakes and you are the one who knows for sure how you want it done and can sometime catch things that are difficult to fix if caught later), but you can take pictures for your photo album (it's fun to go back and look at). Also, you can get "to know" the workers... at least they will see you often and I think people are just naturally inclined to do a better job for someone "they know" than someone who doesn't exist to them.
My mom and her husband took the workers a styrofoam cooler of beer & water on one of the Fridays... it was well received! (Their house was being built in the summer, but it was really nice to get the cold water and beer!)
Anyway, that's all I can think of right now, but I think of anything else, I'll edit my post.
Have fun!
P.