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.
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.