A couple of other observations if they help:
Tried upgrading to level 4 last night. Settler remained lazy and uncooperative. On the plus side now I know not to go for level 4 in any case because that big hanging dolphin blocks my view of my drive-in screen!
Rebuilt the plot using a 'guide foundation' that I scrapped afterwards like in your House Boat placement video (another one I'm having trouble getting the settler to use, but that's more understandable since it's probably a pretty funky navmesh). No luck.
Level 1 fishery seems to have an "invisible wall" around the actual plot space that can't be walked through, even by me? This is about where the shack walls will be when upgrading later, but at level 1 it's just open space. I don't know if it's an indicator of anything that's messing with navigation on later versions but it's weird to bounce off of it.
I very briefly had hope last night when I click-moved the settler inside my level 3 plot, then assigned her to a dance marker I put down. The game reassigned her to the fishery after several seconds and somewhere in that timeframe she sat in the chair!
...but then she stood up and just started standing in place again. So maybe it was just a few seconds where her AI had her as unassigned and she was just looking for the nearest place to slack off.
Also as long as you're looking into navmeshes I seem to have a problem with Tire Cave level 3 where my settler stands forlornly outside the "back wall" rather than going in the very open front to get to his bed.
I love your designs by the way, I wish Bethesda's not-so-great settler pathing worked better. Even kinggath can't reliably get them up stairs in his plots yet!