Always, always, always include a buffer
Whether you are acting as your own general contractor to save money, or you're using the services of a professional custom home builder, including a buffer in your budget for unforeseen expenses is an absolute must. Allowing for miscellaneous expenses is so crucial that I would go so far as to say that if you've received an estimate from a custom home builder that does NOT include an allowance for a buffer or contingency, I would seriously question the validity of the numbers