I think its mostly because the default option is to have the VGA/DVI/HDMI etc on the same side as the backpanel of the mobo...
Given the GPU should be flattish i.e. not take much space it really only leaves the fans on the GPUs to be parallel to the PCB... I think most GPU fans are intakes rather than exhausts (either way)...
So then given all these constraints you can either have the fans facing up and intake/exhaust the hot air from/at the CPU (definitely not a good idea) or you can draw/exhaust the air from/to the bottom of the case and as I said most of GPU fans are intakes... so cool(er) air is more available from the bottom of the case...
And then you have all these fancy tilts to the set up... but at heart the above applies to most cases... Hope this helps
Oh never mind haha I misread your question, I do not exactly know why but I guess it's because the intakes and a possible bottom fan will be in taking air towards your graphics card because the fans are near the bottom.
If I understand what you are saying correctly if the GPU and heatsink/fan where on the other side of the pc board they would be in the road of the CPU heatsink/fan since most motherboards have the primary PCI-E port closest to the CPU socket.