If that's what you're intending, then aren't you better off with ATX? That way if you have the PCIe x16 slot as the top slot and you are going with a 90-degree riser with the GPU facing up, you end up with the card over the I/O backplane area above the northbridge. Granted you'd need a board that has the CPU socket towards the front edge (e.g. front-is-front) of the motherboard so there would be space for the GPU and you wouldn't be able to use a long GPU card as it would infringe on the CPU area unless the board was some sort of eATX form factor. That way the CPU, northbridge and GPU would all be more-or-less inline to the rear fan.
The reason why I'm NOT better off with ATX is because ofthe reasons you mentioned. The combination you suggest doesn't exist, it's just as theoretical as my suggestion.
Good GPU cooling is needed when the graphics card runs very hot, let's say >80 W. Those cards are never as small as you describe.
ATX boards are 245 mm, and hot cards are at least 215 mm, I'm not totally sure how this would work.
However, I think there are bigger underlying problems for hardware companies to worry about solving - for example, why can't we build more efficient GPUs - rather than spending time creating yet another form factor.
That may be a topic for another thread, in the meantime it would be nice to be able to use whatever graphics card I wanted without worrying that it won't be cooled quietly, something that doesn't occur with ANY high end CPU today.
I think it's more likely that we'll see a new form factor that can take a steaming hot graphics card, than the whole GPU industry would make high end cards that never used more than, say, 100 W.
The former could happen today, the latter won't happen for years.
Also, provided you are in a tower format where you don't have to worry about cantiliver effects on the video card, you could install a CPU heatsink on a GPU in a BTX case and have it in that primary airflow path over the CPU & northbridge.
I agree, but then we're back to square one: there are no more BTX made AFAIK. At least not for retail.
I think both the OP and I want the possibility to use two big coolers (think Scythe Ninja) next to each other (just like some dual CPU motherboards), and still have all slots available. No compromising.
Even XBox users can do it, although it's a tight fit