Motherboard design, why oh why?

I built myself a custom small-as-possible case, and whada know, most motherboards are not like the one I designed around. I built my case a few years ago based around a DFI Ultra D with a PCI-Express riser card and a water cooling loop. The problem is it seems like any of the good boards have the "wrong" design and this doesn't work with my case. The water lines have to run over the ram slots in the "wrong" design. I don't think there's enough room above the ram slots for the water lines. You can see that in the layout I like there is nothing (important) there. Yes the case is cramped.

So the questions are,
-> Why do all mobo designers go with the "wrong" design?
-> Are there any good 1366 boards in the layout I want coming soon?

Intel's X58 board: http://www.newegg.com/Product/Product.aspx?Item=N82E16813121361 should work, if you can make your way aroung the heatsink. Still, don't except OCing with that thing, so it's propably not something you would call a good mobo.
As for WHY? Why not? There's more "vertical" space available on an ATX board, and otherwise too, it's more sensible in the traditional way.