If I am going to spend that kind of money on a rifle, I would go custom in a heart beat! That way it will be EXACTLY what i want. It wont just be another gun that a million other guys have and custom rifles typically hold their value better than most factory, run-of-the-mill stuff. They are usually more accurate too!
I don't think that it is necessarily true that custom guns hold their value as well as factory ones - too many variables and also if a person is spending cash on a custom it is desirable to have it customized to your specs not what someone else had custom made. This brings me to the next point - one on which we obviously agree - the big deal about getting a rifle made for you is that it is exactly that: made for you.