Letís not forget that the native species may not have a competitive advance over an introduced species just because it evolved there. I have fished a fair amount in Montana, Idaho and Wyoming. Out there the brook trout is the introduced species and is considered something of a pest. It has displaced native cutthroat in many areas. That is not to say that the rainbow or brown has any competitive advantage over the brook trout in Southern Appalachia.
As for acid runoff in Southern Appalachian streams: not nearly the problem that they have in West Virginia. The freestone streams where our wild trout live are naturally acidic with low buffering capacity, but are not generally in areas that were mined extensively. I do not have the actual records, but remember taking pH and alkalinity measurements on all streams I sampled in the 90s. When comparing to the oldest data we had, we did not see any significant change in pH. The only streams I remember being too acidic for trout were usually the result of a road cut through one of the various acidic shale formations.