I haven't tested it, but my reading indicates that all the MDD and G4 Xserve CPU modules are interchangeable, provided you pay attention to the bus speed (133 MHz vs. 167 MHz) issues.

If the modules ran in machines with the same bus speed, then there are no issues.

Whether the CPU module came off a motherboard which supported booting OS9 is not relevant. It's the motherboard that contains that compatibility/incompatibility, not the CPU module.

Another nice option for the MDD is the XServe dual 1.33 GHz G4 module. There's a seller on Ebay with new service parts for $75, which seems a bit steep considering that they don't include the heat sink.