Seems a little backwards to me to design your case and then design the motherboard to fit inside it, but I've never built any laptops so I'll just watch and see where this goes.
This is Olimex's blog, and they design and sell dev boards, so it makes some kind of sense to leave the part that you have full control over to the end, I suppose.
Tooling for injection molded plastic is very expensive so for small-volume runs like this one it's likely cheaper and quicker to get off-the-shelf plastic.
The proper way would be to build all parts to fit each other, so you got everything done properly. I imagine that is how Apple does their things anyways.
You have to start somewhere to be able to set your constraints. If you already know how the hardware works and what will be required there. It makes sense to do a gross estimate for the enclosure and design a board to fit.
