Is this technology viable for structures still in use, specifically, flood control structures with stop logs?

Yes. However, a screw installation takes water from the top of a water source and has a fixed installation point.
Therefore, when stop logs are removed, generation can cease if the water is lowered enough to cut off the water supply to the screw.

If stop logs are removed for significant periods of time this can seriously affect the financial return on the project. To overcome this problem automated dam sluice gates can be used to maintain water intake height.

As flow increases, the automated sluice gates on the dam structure open to allow more flow and keep opening as long as water intake height is maintained.