According to the manufacture's site, this mobo works for 2xSLI or 3xCF. I think that the first and the second PCI-E slots are intended to be used for 2xSLI and that all three PCI-E slots are to be used for 3xCF. So maybe it might be OK to use the first and the third PCI-E slots for 2xCF but not for 2xSLI (although the third slot is slower than others). You should ask MSI directly to clarify this issue.
G45 Gaming z87 is supposed to work at 16/0/0, 8/8/0, or 8/4/4. Meanwhile GD65 Gaming z87 is supposed to work at 16/4/4 or 8/8/4. It seems to me that the third slot is active regardless of how you use PCI-E slots in GD65 mobo. On the other hand the third slot seems to be inactivated in G45 mobo at certain configurations. You can't just say that G45 mobo should work in your preferred configuration just because GD65 mobo can do. You had better contact MSI to clarify the issue.
No use contacting the manufacturer.. The specs for the MSI Z87-G45 Gaming Motherboard are: That board is what it is. The 1st and 2nd slot are shared. The 2nd and 3rd slots are shared. Even if you use 1st slot and 3rd slot your 1st slot will run at 8x While the 3rd slot will run at 4x There are 16 pcie 3.0 lanes and that's the way the manufacturer has done things with this board. They have followed the specs of the CPU and offered exactly the 3.0 lanes the cpu offers. Nothing can be done, buy a different motherboard or use slot 1 and 2 for 8x/8x or run in 4x/4x using slot 2 and 3 or switch to crossfire set up .
