As of right now, it's not possible to change floor's height in Arnis. I tried using the minimum possible scale, and got really tall, but really thin buildings. The solution? 2 options. First - 'Window height', which by default would be set on 3, and 'Gap height between windows (Y)', which is by default would be set on 1, as seen on a buildings, that Arnis makes. (one floor is 1 random block, then 3 blocks of glass, and then another block, and so on).
How it is (on min scale) in-game, and 4 different sets of options - see the 2 images (for sets of options, W - 'Window height', G - 'Gap height')