I like your thinking.
Only fished it for salmon a couple times many years ago. Seems it might be worth a shot though. My Dad caught a very bright Chinook once, just downstream from the bridge slow trolling herring. Based on that single data point it would seem they actively feed, and are hypothetically receptive to flies, at least that far up the bay.
To my limited knowledge, the lower bay, and along the jetty are the more productive areas - and I understand why you'd want to try there. The challenges there are strong currents and concentrated fishing pressure. Short of trolling flies on heavy heads, I'm not sure how you'd effectively mix fly fishing with other boats trolling.
If it were me, I'd lean towards finding some staging fish further up in tidewater, anchor up and fish comet type patterns.
I've also thought about fly fishing off the South jetty since the deepest part of the channel is right against it, and the salmon should be within casting range. The problem there is that's one of the steepest, most dangerous jetties I've been on. Landing a big Chinook on fly gear would be sketchy to say the least.
Good luck!