Currently I've restore the old config.plist with MacPro3,1 and it can boot normally again without nv_enable nor nv_disable boot args. So I'm pretty much sure there's something not compatible in the config.plist that prevents the kext detection.
But I'm still curious about Sierra. Later on, I'd like to try exchanging the Mac model once more then post here the differences.
Since I just resurrect my old rig using this graphic card, I'm expecting a solution for the HDMI sound if any. I hate to use again the audio jack since the HDMI audio used to work fine in Mavericks, and my wall is already messy with cables anywhere.