If a nice off-the-rack store bike fit me comfortably and had the features I wanted, I would buy it happily and not have to wait for a custom to be built or go through the custom bike 'communication dance'.
But I couldn't find the kind of stock bike i wanted that would fit me right. So I got custom.

Three reasons to buy custom:
1) You need a particular frame geometry in order to feel comfortable.
2) You can't get the combination of features you want from a stock bike.
3) You have the money and like the idea of having a bike made just for you (some might call this merely vanity, but justified or not, it's still a reason).

If none of these reasons apply, don't get a custom bike made.