I own a "Custom Home". It's a one-off that was built in 1994. My wife's dream was to own a custom home, so that's what we purchased in 2003. I only have one word to describe a "Custom Home":
Now, you are at a major advantage because your family would be participating in the construction of your home, so it's less likely that you'll encounter "weirdness" in the home design and decisions. But we've had whoppers here, from a single 75 gallon hot water tank on the second floor that feeds a floor above and a floor below (which generally means the bathroom faucet, tubs and showers have to be on a minimum of 2 minutes before warm water is feed through the pipes) to having 10 electrical outlets and eighteen 6" 75 watt can lights on a single 15 amp circuit to literally dozens more bad examples.
I could go on and on about all of the repairs and changes I've needed to make to this home for the past 10 years (and in excess of $200k) but I'm sure you get the point. While I absolutely love my home, there have been days when I wished it were not a single, one-off, custom home because it's likely to have been better designed.
Whichever way you go, best of luck!