That's not the reason your SATA ODD ports aren't being recognized. If it was, you could just change the SMBIOS back down to a 2,1 and they'd work.
The SATA ODD ports get initialized based on your DSDT settings. If you were to boot Chameleon without your DSDT, you'd find exactly the same behavior you are experiencing with Clover. For some reason, Clover on a real Mac Pro doesn't process the DSDT correctly. Chameleon did, so people didn't bother to figure out how to make Clover work right on a Mac Pro. Now, depending on how long it takes Chameleon to sort out the Yosemite kernel (my prediction: the kernel structures will be fully supported by July 4th) people may spend some effort figuring out how to get the Mac Pro hardware properly recognized on Clover. I bet it's not a difficult fix/workaround, so odds are good Clover will work with a Mac Pro, especially if Chameleon kernel work takes longer.