Hey Daedelus, thank for your support

You could make a file with room objects that are placed seperately, as HeroQuest furniture is.
I begin to think that this would be the best solution to allow customization. On the other side, a fixed layout also allows the creation a of random generation system and also a quicker settings. I'll provide both I think.
Variations in the board size
My initial objective was to create a whole city tileset made out of squared tiles, so that everything fits, I'll keep that layout.
The isometric view of the inner walls doesn't seem to be working as well as the bordering walls.
Yes I see what you mean, and I think i'll go with simple 'black' walls.
pattern, and color could help do this. Maybe some dirt floors, or tiled ones
I have a pretty clear objective : create everything needed to set up a city : house (noble, poor, normal), taverns, shops (alchemist, armory, etc), prison, market place (shops, horses, wells, etc), temple, docks (boats, entrance to sewer, etc), guard's tower, prison, Castle walls, Castle...............

The most difficult things is to find/create appropriate furnitures, textures.