With regards to hidden staging I really want to keep all the trains visible and run them from the yards. Even if a few people are running trains, they can setup at different stations and go from there. Running the Barry beach train may have to start from KooWeeRup.
So the daily Yarram pass will run from KooWeeRup, around the layout back to KooWeeRup, stand there all day, run around, and then run back? While I can understand that it's nice to keep things in the open (and the Dutton Bay has open staging) it's going to be really hard to convince people that a train from Melbourne starts and ends at KooWeeRup in both directions.
If you were modelling a self-contained line then you can get away without staging. But you are only modelling a small segment of a line, and wish to be able to operate in a realistic manner, then trains which start or end beyond the layout really should start and end beyond the scenic portion of the layout.
I would certainly keep KooWeeRup, but it's only a small station, and was not a terminating station (at least in the last fifty years) so keep it as a small town station. It makes a nice station at which you can cross trains without it being cluttered with terminating trains.
Open staging between KooWeeRup and the door could represent Melbourne and Yarram. Perhaps with a light scatter of ground cover so it doesn't stand out like a sore thumb in a nicely sceniced layout, but it will increase the operating potential of your layout enormously.
It's your layout, you can and should do what you want, but it's worth considering why almost every layout of similar scope to yours has staging. I've operated many layouts and except for a couple of narrow gauge self-contained tramways, every one has had off-scene staging.
But whatever you do, I would like an invite to an operating session one day... your plans look very good.