The biggest difference is that in the factory setup, the pump is pushing the fluid through the entire system, such that on the inlet side of the pump, it is being pressure fed. In fact, if it were not for pressure losses by moving fluid through restrictions (hoses are a restriction due to friction), intercooler, HX) the inlet and outlet pressures would be identical, and no flow would occur. Anyways, back to my point, there is positive feed pressure on the inlet of the pump thus no air bubbles (if properly bled) and the system works fine.
https://www.ctsvowners.com/forum/71-cooling/5979-hx-flow-pat...