Personally, I'm on the hunt for a Dual Proc tray as well for my 4,1. As others have said, as long as the tray is from the same model, you'll be fine. Luckily there is a way to tell them apart if the heat sinks are removed.
Since I got my Mac Pro on an absolute steal of a deal, I really had no choice on the processor tray. It also had no RAM or video card, but thats besides the point. What I have done is flash the firmware up to 5,1 and swapped in an W3680 (6-core, 3.33GHz, 12MB Cache). A huge upgrade from the original W3520 (4-core, 2.66GHz, 8MB Cache).
Trust me, these machines are more then capable. What I love compared to the new Mac Pro is the fact you can upgrade almost everything. PCI cards, HDDs, heck, someone even found a way to upgrade the original AirPort Card to a newer one with 802.11ac and Bluetooth 4.0 LE so you can use Handoff/Continuity with the machine. I have 4 hard drives in mine, 1 PCI Card (USB 3.0), upgraded optical drive, up'ed the RAM. If you are a computer guy, these machines are just a blast to work on. I love mine and I would never sell it.
I'd like a nMP, but I will forever hold onto my cheese grater no matter what.