you have to understand that wind is not the only thing that causes choppy seas. in puget sound, strait, and entrance to the pacific the current has a huge impact on the state of the water. forcing yourself to troll if it is not flat calm is imo the very definition of a boat not meant for fishing the pacific northwest.
there are plenty of non self bailing boats that are far better northwest boats than a flats boat. the decking all over is one of the problems with a flats boat. freeboard allows you to fish comfortably anywhere on the boat (front, back, sides) without worrying about a freighter's wake sending you into deep, cold water. the coast guard testing is impressive, but not very relevant to what makes a good pacific northwest saltwater boat.
I don't feel forced to troll until the seas are 3 foot which is far from flat calm to me. What is the concern about the freighter wake: is it that the wave will rock the boat and someone will fall in or that the wave will swamp the boat? If the concern is falling out then yes higher gunnels will help to keep you in the boat, but sometimes falling in the boat causes much greater injury than falling out of the boat if you're appropriately dressed to take a swim. I am very comfortable standing to make a cast in the front while bracing my knees against the bow platform and then sitting on the casting platform for the retrieve if it's really rough. No matter what vessel you're in, it requires constant attention to fish in rough conditions.. A deep vee center console is very unstable at rest and it can be tough to keep balance unless you're wedged into both gunnels at the bow. Midships without a coffin box is like a 6' by 10' dance floor on a tilt-a-whirl when a big boat wake goes by. Without decking, a wave that breaks over the transom is now in the boat and it takes the bilge pump several minutes to clear the water compared to two minutes for a self bailing cockpit. You're also just one bilge pump system failure (pump, debris in pump, debris in discharge, hole in discharge, battery) away from a proper swamping. The decked over boat probably has 10% of the water in the cockpit compared to what a center console would have.
a 16-18 ft center console with decent freeboard is really easy to pee of of... and you can take a piss of the back, front, or sides of the boat in chop.
I'm 6'2 and I find the freeboard in those length boats to be enough to keep me in the boat but not really comfortable to lean into for balance for fishin or pissin when it's rough. The poling platform hits me at the waist so I can really lean into it for casting and it's at a perfect height to grab with a free hand while whizzing.
getting out of the weather is nice, but not all that important for fly fishing. a fishing boat is for fishing, and a center console with freeboard is perfect for the pacific northwest. as for mounting dowriggers, if we're talking about fly fishing boats that's not relevant.
most people also want a boat that can be used in many different fisheries. they might want to fish for pinks in the south sound, cutthroat in hood canal, coho and rockfish at neah bay, and maybe trips to vancouver island. having a boat that really works well for very shallow water fishing (which we have very little of) just doesn't make sense for someone who lives and fishes in the NW.
The reason for possibly wanting to mount downriggers is just that: flexibility in uses for the boat. I don't always fish in saltwater, and when I do I prefer to fly fish

To me there's a world of difference between a multi purpose flats boat that can handle rough water and a technical poling skiff that is designed only for really shallow water. The poling skiff is definitely a questionable choice outside of the flats, but a multi purpose flats boat is really only good in 12" or more water and is just an excellent casting platform at rest in 1 foot or 500 feet of water. To me that describes what's best for all the fishing situations you mentioned. The trip across Juan de Fuca I imagine would only be attempted on flat calm or close to it days in a boat less than 20 feet regardless of its hull type.
there's a reason there are virtually zero flats boats fishing in the pacific northwest.
I agree, that means either it's been tried and it doesn't work or no one has tried it. If it's been tried then please provide some links to some horror stories of bad boat purchases or flyfishermen lost at sea.. The only thing I've found online on a northwest flats boat is this JohnK guy from Port Townsend sounded real happy with his Scout 177 flats boat:
http://www.thehulltruth.com/boating-forum/12183-john-k-washington-new-scout-177-a.html Too bad there aren't any reports after the first one or two. Has anyone seen him out there? Maybe he did get into trouble in his brand new boat.
There were virtually zero flats boats in the northeast too until people tried them out and found them really useful. The Pacific northwest is even further from Florida where most boats are made so it might take longer for them to reach the left coast. The lack of shallow water does make it even less likely for a flats boat to move there automatically. A flats boat isn't a general purpose boat like a center console for trolling or family cruising which means it would take someone interested in only casting to try one out. Just because no one has tried it though doesn't mean a flats boat couldn't be a great choice for an at rest casting style of fishing.
I would be very interested to get opinions based on actual experience. In this case I know I'm speculating on pros for performance based on a lot of time on a flats boat (over 400 days in the last 5 years) with limited time (maybe 30 days in the last 5 years) in the Northwest and I'm guessing you're speculating on cons based on a lot of seatime in the Northwest and not much on a flats boat like an Egret. I know for sure I was wishing I was in my Egret when I rented the fly fishing designed 17 foot skiffs at Weigh West in Clayquot. If you're ever in south Florida let me know and I'll take you out for a sea trial in a flats boat that's not a technical poling skiff. It might not change you from a no to a yes, but I bet I can get you to maybe.
martyg: If you're looking at a remote flats boat that claims to be self bailing I think it would be worth putting a post on floridasportsman Boating forum to get details from people that have been on the particular boat as to just how the self bailing is implemented. Lots of the flats boats claim to be self bailing but as soon as the boat stops moving and you have more than one 150lb person in the boat, water comes back in through the bailing holes. Most of those boats offer plugs / shut offs for the thruhull. Egret has a goose neck from cockpit to thruhull and is totally self bailing at rest even with a thousand pounds or more of stuff ( 3 big guys going camping) into the boat. They don't offer a plug for the thruhull because it's not necessary. That coast guard test shows you can't get more than 3 inches of water to stay in the cockpit even if you completely flood the entire rest of the boat.
Smalma: you got a special custom trolling motor there?

Minn Kota Rip Tide is either 101# thrust and 36 volt or 80# or 72# thrust and 24 volt as far as I'm aware.