I prefer to think the reason 48 heads were used on the 1969 Pontiac 350 was because of the "me too" sales policy. The "me too" sales policy was to compete with the 1969 Chevy Z28 on the showroom floor. The 48 heads are some of the best heads you can use but only on a 400 or 455 engine.
All successful performance engines are "over-square", meaning, the bore is larger than the stroke. I cannot think of one thing a Pontiac 350 engine would be good for except for fish structure. You cannot even bore a Pontiac 350 engine so it will accept high performance heads. The "under-square" (small bore) of the Pontiac 350 severely limits its RPM potential.
There may be a rare occasion that a Pontiac 350 engine will be competitive at the track but I don't see how they can be compared to a Chevrolet 350 "over-square" engine.