The reason there are few populations in PA is that the strain of rainbow raised and stocked by the PFBC is a highly domesticated strain that tends not to establish wild populations. Which is a good thing because wild rainbows can out-compete native brook trout far into the headwaters, as they do in the Smoky Mountains.
In other states, their hatcheries have different strains of rainbow trout, that can establish wild populations.
The rainbow populations in PA were mostly introduced through private stockings. A few streams in NW PA have populations that are usually attributed to stocking by a federal hatchery.
The reason there are few rainbow trout populations in PA is not because of stream characteristics. There are rainbow trout in both limestone and freestone streams in PA, and streams similar to ours in other states in our region.