I think the actual passage at the lower dam was always narrow and rather high velocity. If memory serves there were issues with old rebar still in the river. I suspect that even when it is cleaned out that the action will be a velocity barrier at some flows, especially for smaller fish.

This pinch point os likely one of the reasons that Elwha Chinook were so large. Arriving during the higher flows of the snowmelt season required brute strength to pass.

Further, when the lower dam was first installed it blew out at the bottom. The hole was filled with logs and other material. Which suggests that there is a lot of junk remaining there. Plus, all the accumulated sediment from above has to pass through on its way to the Straits. Some may decide to sit a spell.