The problem with ITX (or even mATX) cases is this, if you want to keep a small overall footprint:
- If the optical drive hangs "over" the motherboard, then the case becomes high
- If the optical drive is positioned to the "side" of the motherboard, then the case becomes wider, but potentially thinner.
My perspective is that it's a compromise and an individual choice. Some folks like thin cases (but don't mind wide), some like them narrow even if they are higher.
An ITX motherboard is 6.7" x 6.7". Even though optical drives (full size drive that is)have varying depths, most modern drives are never more than 7" deep and 5.25"-5.5" (approx) wide. A 1U server chassis (1.75" high) easily fits a full size drive. As far as motherboards go, a fair number will fit, other than a few whose audio headers on the back panel are too high. Then you need to think about the one and only add-on card that you may want to add to the system. The "height" of a full size add-on card is 4.2"
So, let's start designing a case....

Case width = 6.7" (MB) + 4.2" (add-on card height) + 5.25" (optical drive width) = ~16.2"
Case depth = And that's where the design forks out into any number of configurations....
Case height = Has to be atleast ~2" and onwards....And that's also where the design forks out into any number of configurations....
Where do you put the power supply? What type? What size??