True, but Apple has control over the entire process -- ever notice how all of their motherboards, from the G2s to the G5s, have different layouts? They can build 'em to spec, and have been doing so for a long time.
As for PC motherboards, just about everyone uses the same 2 or 3 form factors -- compatibility is key here, not a nice-looking case.
Just because Apple uses Intel chips does not mean they'll use standard ATX form-factor motherboards.
While I agree that the internal configuration depends on things other than how meticulous the assembler is, there's a lot you can do if you spent some time. There's no excuse for the Windows computers with wires hanging everywhere, ribbon cables running this way and that and general lack of attention to internal layout. I believe that if Mac users could build their own generic Mac system, the majority of their internals would look similar to the average home-brew PC: messy, cluttered, not thought out. There are only so many ways you can route a hard drive cable, but there will always be a clean, nice-looking way and a sloppy, lazy way.