EFI Firmware Update 2.0 for Mac Pro - is not compatible with my Mac Pro 6,1

Don't install it. Perhaps you did not download the proper file or the update has already been done. Mac Pro EFI Firmware Update 2.0.

About this Mac > ( More info ) > ( System Report )

These are the up-to-date versions you should be running:

Mac Pro
Mac Pro (Late 2013)	MacPro6,1	MP61.0116.B04 (EFI 2.0)	2.20f18 (SMC 2.0)
Mac Pro (Mid 2010)	MacPro5,1	MP51.007F.B03 (EFI 1.5)
Mac Pro (Early 2009)	MacPro4,1	MP41.0081.B07 (EFI 1.4)
Mac Pro (Early 2008)	MacPro3,1	MP31.006C.B05 (EFI 1.3)
Mac Pro (8-core)	MacPro2,1	MP21.007F.B06 (EFI 1.2)	1.15f3 (SMC 1.1)
Mac Pro (Original)	MacPro1,1	MP11.005C.B08 (EFI 1.2)	1.7f10 (SMC 1.1)

from:

EFI and SMC firmware updates for Intel-based Macs - Apple Support

They are probably already installed.

Check your firmware version

Check your computer's EFI Boot ROM or SMC firmware version.

1. From the Apple () menu, choose About This Mac.
2. Click More Info.
3. For OS X Lion, OS X Mountain Lion, and OS X Mavericks, click System Report. For earlier versions of OS X, skip to step 4.
4. Click the Hardware section to reveal Model Identifier, Boot ROM version, and SMC version numbers.
5. The version information is in the pane on the right, as in this image:

.

check you boot rom version using ASP; if it show ending in 07 rather than 04 then you cannot use that EFI firmware updater.