Well, again, it does not work that way.
I'm well aware that 6x means 6 lanes for a PCIE slot, but in the same sense, you really can't stack 2 3x slots together and call them a x6 slot. It's like saying you can take 2 different train tracks that go to different stations and make it so that all trains going through those tracks end up at the same station.
Yes, it's possible... but the technology to do that is unnecessarily complicated (you need a linker) and it's just to solve a problem that shouldn't be there in the first place (if you have access to a single x6 slot). That's why it doesn't happen.
Similarly, they'd need a dedicated chip and some pretty elaborate hardware-software interplay in order to make 2 x4 slots stack together as a single x8 slot. The whole thing is so hard to achieve (especially since you know how Apple does not play nice with features they don't condone) that I might as well write "it doesn't work that way". Not that it's impossible, but that nobody would bother.
Is it clearer now?
Otherwise you'd think they'd have come out with a Thunderbolt to x8 adapter already:
http://www.sonnettech.com/product/xmacminiserver.html
Edit: or let me put it a different way: since the discussion involves an Apple device, of which the drivers are partially (or totally) controlled by Apple, it might well be "impossible" to achieve unless Apple themselves start supporting the idea.
Even then, it's a big mess to solve a "problem" (that should not exist) for a small niche.