when you have more cards and more PCIe motherboard lanes being used you need more bandwidth over the pcie bus... you have the equivalent of 2 cards on the motherboard so you aren't taxing the pcie motherboard lanes anywhere near as much as 4 GTX 680s would be, your resolution also isn't requiring enough bandwidth to make a difference
the results posted above are both on the same cards and the same resolutions, so VRAM limitation isn't a factor as both setups have the same limitation - yet pcie3.0 makes a massive difference in that setup (4 individual 680's)
4 individual cards all need to talk to each other over the motherboard, where as 2 690's halve that requirement because 2 of them talk to each other directly and then each pair shares the data sent back and forth over the mobo
if you can't see why 2 690's need less bandwidth than 4 680's then I really struggle to be able to have a conversation with you on the subject
pcie bandwidth only becomes and issue (e.g. possible to show an improvement) when you are reaching the limit of that bandwidth... from the graphs on anand it is clear that 4 individual 680's at x8 speeds need more bandwidth, where as a single card or even 2 dual-gpu cards (Running at x16 by the way) don't need more bandwidth