I had some trouble with my internet connection, so this is coming late now.
I had a try on the map:

- Besides the winch I only have added one spiral way up/down upper Quintherion. Its placed central on the hollow plaza tree, main purpose is a direct way to the garden, without having to occupy the winch. I think every tree having one would take away the advantage of the protection houses sitting up on a tree would provide.
- Watchtowers are nothing but appropriate fortifications on trees. Those two ones in the east may be (or influenced by) ylian architecture, to accent the newer part of the city.
- The city walls would appear from the outside mostly as a very thick and dense forest for achieving camoflage. Its line would be irregularly. From inside you can think of it as plane-objects, textured by leaves-images, while now and then there were windows like the ones in the secret garden in hydlaa. After all its dermorian and some magic may be involved.
- About the area west/south-west on ground level, which is currently "empty" could either do for keeping goujahs or other domesticated cattle, or also a part of it could be for the storage area. Also the vegetable garden could be extended. Not sure yet.
- Major 2 sections: New Quintherion (plaza, housing, winch); Old Quintherion (garden, central plaza, housing)
- Given dimensions are probably understated..
I also gave a quick first shot on a hut sitting on a tree. Besides the dodgy quality the hut may be too much like a tent, unstable and weak. Main idea was it, to have one house having more than one level. I also think some similar way could do for having multiple levels on one tree, giving it an organic, like grown, look.

Now I got some questions:
1. "A few buildings, like the vigesimi's house, are constructed of wood.": I assume the very biggest part of all houses, the common places to live that is, are built of vines and leaves only, right? What other buildings would be of wood as well? Single ones of rich people?
2. "Quintherion has two smithies": If those are meant to be original Quintherion ones they are placed in the upper city?
3. Those ylian houses are private places only, for foreigners not comfortable to live up on trees, yes? So at the ground level plaza there wont be much activity, maybe some trading of the woods stored there, or some concerning animal products? But the most crowded and active place is the central plaza on the hollow tree's platform, right?
4. 3000m² max? Are you serious? That would be 55mx55m. Considering the size of the Hydlaa-Winch "Temple" (that would almost fill up that dimension), each of these 3 cities wont be very.. big, huh? Or eh.. did I make some fundamental mistake here? lol If thats still a strict rule though, I could move the Veg-Garden completely onto the ground level beneath the upper city, and move the whole ylian-section to the south a bit (for still fitting requirements).. Hm, may I will give it a quick try anyway o/
EDIT:
So now I rearranged it a bit.

With same dimensions as above, everything will be quite a little bit bigger (although fix point was the hollow tree with 7m diameter, and the central plaza with 22m).To use space efficiently, why not having trees growing inside the garden.. as long as theres still enough room for growing roots.. after all I wouldnt think dermorians go for geometrically ordered gardening, clean and sterile, would they?=P