This looks like a really fun
This looks like a really fun concept! I have visited Vancouver once, and I left with lasting excitement about the waterfront railyards, despite having hardly a clue at the time of how Vancouver's rail terminals were laid out. Since then, I've been reading more and more about them.
I have a couple ideas, from least to largest effect on construction:
1) Would you benefit from having at least one staging track? I know you plan to mostly do switching, and I find it helps to have a place to originate trains. You also mentioned continuous run, and I know I like having a place to store all of my trains! Even just one staging track, let's say hidden along the back wall, could prove very useful, and it would require minimal maintenance since you wouldn't need to have hidden switches. A more involved version of staging could involve dropping the railroad down a level on the return loops, and having more staging tracks on a lower level along the back wall. Building it wouldn't be difficult, especially since it doesn't look like you plan deep scenic cuts (just enough to get down to water along the wharf).
2) If you were to implement some sort of staging, would it make sense then to rework the plan to not need to separate the terminal tracks from the switching tracks in front? It looks like you've got them separated to avoid tiny reversing sections. But, if you added some form of staging and then un-separated the two sections of visible track, then you'd have something perhaps more closely resembling the prototype track arrangement actually.
3) Module sizes: I noticed you're planning a bit in terms of modules, which suggests perhaps you want to be able to move things in the future, which is great. Since your plan will require lots of tracks across the module boundaries, which can be a bit annoying to plan for (learned that from experience), it might be nice to reduce the number of module joints if possible. Have you possibly experimented with the longest table you can do while still being able to get it up your stairs? That might be useful, to see if you can maybe turn the three middle modules along the wall into 2, meaning one fewer joint .
4) I had a couple thoughts to throw out in terms of the overall benchwork footprint, which you may have thought of already and ruled out, but I want to make sure you heard the ideas:
4a) It looks as though you have enough space where the optional 4th phase pier is, to move the left-end turnback loop there. Then, your track could wrap along the optional section, giving you a bit longer run. Not sure if this is a gain over the existing plan from your perspective of the piers and traffic. You could turn your workbench 90 degrees so that the chair faces "up-diagram" to make that space available. You'd lose a bit of free movement space for operators though.
4b) Have you considered making it more of an around-the-room plan, rather than using the turnback loops? You could do it across the middle of the room, and do a lift bridge for access approximately where the foundation support pole is - a lift bridge would be easy to build, and you could keep it open while doing construction, and close it only when operating. Or, you could even potentially elevate the railroad enough that a nod-under wouldn't be problematic: I do a nod under on my layout, and I really haven't minded it at all (whereas I hate duck-unders with the fiery passion of a thousand suns). And, even more extreme: could you wrap a track all the way around the walls of the room, behind the furnace and the stairs? Crazy, I know - I only suggest this last possibility because it would make fitting your piers in the middle of the room really natural, because of all the space you free up from the turnback loops.
5) Here's one wacky idea that you might want to shoot down out of the gate: Is there any value in flipping the plan such that the wharves are on the wall? The reason I say that is, I remember the wharves have lots of tall objects like elevators (at least today). Those sorts of things are particularly well suited to backdrop buildings (though, to be fair, they're super impressive when they're out front). And, then you also could have the towering Coast Mountains in your actual backdrop.