I have not found that to be true at all. It's true if you go with a high-end custom pc builder, but you can often get a very respectable desktop prebuilt for less than the cost of equivalent components.
I guess it also matters what we define as a prebuilt. Some prebuilts are just standard components assembled (hopefully competently).
Some prebuilts, especially from Dell, HP, Acer and Lenovo will have custom motherboards, custom power supplies and custom cases that can't be re-used later on. Those usually have the very crappiest cooling solutions too. So they will end up costing you more money down the road, because you can't incrementally upgrade the pieces as much as you could with a self-built PC.
