Regarding zone generation, here's a hypothesis:
The area of an L-shaped map is 108x108 = 11664 cells.
The areas of the zones on the template are: 31*31 + 33*33 + 32*32 + 34*34 + 15*15 + 4*4 + 7*7 + 5*5 + 6*6 = 4581 cells.
The RMG simply starts adding zones until the required area is reached, sometimes crudely, at the expense of one zone. This is where the imbalances come from. The sum of the areas of the zones should be approximately equal to the area of the map.

Not quite. The generator initially plans the zones as circles with a specified radius, and then, if they intersect, it somehow trims them. This is clearly visible, for example, in the Dungeon maps.

Therefore, yes, when developing a template, it is necessary to select the optimal size of the zones - on the one hand, so that they are not too crowded, and on the other hand, so that there are no large dark spots in the underground or sharp imbalances in the sizes of the zones.