There are good reasons to buy custom and good reasons not to, depending on each riders''s wants and needs.
I wouldn't buy custom because my fitness level changes so much---I cannot be sure that a perfect fit today would work at all six months from now. I would need to be swapping stems, bars, spacers ....
If I still rode a lot, I would get a custom Ti bike tapped fro custom racks ... and Arkel panniers, which i have wanted forever .... but for now, I can still haul the groceries with my cheap Nashbar bags.
If I raced a $7 K bike, knowing how long race bikes might last (rules change, crashes happen, miles definitely add up, and the bikes get transported a lot) I would already be a little uneasy. Each to his own.
My current "fast" bike is a Chinese clone of a last-generation Cervelo R-series. It has weird tube lengths---in particular a tall head tube, for a racy frame---which make it ideally suited to my weird body. if I lost it, I doubt i could buy a bike off the shelf which would fit me .... but i am not sure i could justify the cost of custom carbon.
if however, my bike budget was eight grand instead of $2200 .....