It's because the engine design dates back to the Nash. Inlines aren't immense power motors, and casting the ports all on one side allows a single gasket to seal it. In the days of carburetors, it was also easy to heat the underside of the intake with the exhaust to promote vaporization. With MPFI, it's not necessary as much. It also makes placing and routing the distributor easier.
The Dodge Slant Six, Ford 200 and 300, Chevy 250, etc all used the same side of the head, IIRC. And yes, it isn't the technically superior way to do it for high horsepower - but a Jeep isn't for that. High velocity cross flow heads aren't optimal on low revving torque spinners.