You can test an early-2009 component with a mid-2010/mid-2012 Mac Pro and vice versa.
The issue is that the early 2009 backplane and CPU trays have the SMC microcontroller programmed at the factory with SMC firmware version 1.39f5 while the mid-2010/mid-2012 have it at version 1.39f11, these two versions are incompatible with each other and when you install an early-2009 CPU tray to a mid-2010/mid-2012 (or vice-versa) the SMC from the backplane can't talk with the CPU-tray SMC, the mismatch will make the SMC enter fail-safe mode and run all fans at full speed, but that is not a problem for testing parts.
You can't upgrade the SMC of the early-2009, can't be dumped and the 1.39f11 SMC firmware never leaked from Apple.
Everything else inside the case is completely compatible, you can use every other component as replacement parts or to test without any adverse effect. For example, you can install an early-2009 PSU to a mid-2012 Mac Pro, no problem.