There are many variables you are not considering that make impossible to objectively compare YOUR GPU performance for a dual GPU setup simply by comparing PCIe lanes on a motherboard.
The PCIe lanes are not used for processing, only for data transfer meaning while bandwith might be correlated to graphics performance, they are not directly related. Half the bandwidth may NOT mean half the performance.
Both boards are using the same chipset with only 8 PCIe lanes through the chipset. Intel Z97 Express Chipset - ark.intel.com/products/82012/Intel-DH82Z97-PCH. This means that access to CPU processing power and memory is the same on both boards which would affect GPU performance, but at an ukown amount.
Performance will also vary with application; that is what software you are using, and how the software uses the GPU, CPU, memory, etc. will affect real world performance
And finally, SLI and Crossfire add there own variables in that some applications do not take full advantage of both GPUs like on would hope hampering performance. Again, this is both application specific and hardware specific.
I suggest you take a leap of faith and just do your research, eliminate what variables you can, leave the variables you cannot, and hope for the best. Your GPU performance with a dual GPU setup is a variable you are not going to be able to nail down without real world testing and benchmarks on your hardware with your applications.