I think I can answer the question now. There was a misunderstanding regarding the firmware upgrade tool to upgarde a Mac Pro 4,1 to 5,1. The firmware upgarde tool does not update the SMC firmware, but installs a different boot rom version.
Mac Pro 4,1 (2009): MP41.0081.B07 (original)
Mac Pro 5,1 (2009): MP51.007F.B03 (upgraded)
The system and CPU board SMC version remains at 1.39f5 for the MacPro 2009. A Mac Pro 2010 uses 1.39f11. After upgrading a Mac Pro 4,1 to 5,1, the SMC firmware was still 1.39f5. SMC mainly deals with temperatures and fan speeds. It is important that the SMC version of the CPU and system are the same.
So to answer my question, it is not possible to use a 5,1 CPU board in a 4,1 system or vise versa. I'm not sure what happens when mixing them, but apparently the system does either not boot or the fan's go crazy, perhaps depending whether you put a 5,1 cpu board into a 4,1 system or vise versa.
Here are some links I found meanwhile for reference:
http://forum.netkas.org/index.php?topic=852.0;wap2
http://forum.netkas.org/index.php/topic,852.375.html
http://arstechnica.com/apple/2011/05/firmware-hack-can-transform-a-2009-mac-pro- into-a-12-core-monster/
Btw, the firmware upgrade tool 4,1 to 5,1 shows error 5570. That is because Apple changed the location of the 5,1 efi firmware image. You can however download the 5,1 firmware form Apple and simply mount the disk image prior to running the tool and it will work fine. Then shutdown the system and hold down the power button until a tone occurs, then the system will restart and show a progress bar to update the firmware.