Is a MacPro3,1 (2008) x16 slot PCIe 2.0 or 1.1?
If that is a PC (non-EFI) graphics card, running it in Windows on a Mac (Bootcamp) will reduce the speed to PCIE 1.1

You must have an EFI flashed card to run at PCIE 2.0 in Windows on Mac machines. Drivers solve this issue for some PC (non-EFI) cards in OS X, but not Windows.

Real world gaming difference between 2.0 and 1.1 will likely be negligible, and your bottleneck will most likely end up at the CPU or OS X drivers. Generally I see better performance in Windows.

For reference I run a GTX 1060 (non-EFI) on a 2009 Mac Pro; my benchmarks and real world gaming are all better in Windows, at the PCIE 1.1 speeds.