Hmmmm, How have Skamania summer-run fish affected winter-run fish in the Toutle, or for that matter the Washougal? I'm having a problem with your logic. If the Skamanias are not good reproducers, then how are they going to take over a run?
My home river is the Skykomish, and the hatchery summer-run over most of the 90s have been outstanding. In most years, the hatchery got its escapement before August and in December it was a toss-up of whether you were going to hook a mint-bright winter brat or a black summer-run at Reiter (Reiter Ponds Hatchery drift). None of these remaining hatchery summer-runs were collected by the hatchery and most anglers were releasing them because of their color. Presumably you had a lot of them spawning in the main river over many years of the 90s. Yet, every year I catch less than a handful of native (unclipped) summer-run fish, indicative of the very small run of summer fish that historically used the basin.
These fish have not likely mixed with the native winter-run in the Sky either, because of very little overlap in spawn timing.
What is the mechanism of disruption that causes the problems? From what I've heard, both the summer and winter-runs (native) on the Washougal have been depressed for some time now. Could there be another reason for the declines, like logging/development? I really don't know that area, but they plant Skamanias in a lot of Puget Sound streams that have enough water during the summer, and there appear to be minimal interactions.