Nope that isn't it, the chassis from the ebay offer has a SAS2 backplane, so not the "B" version. The "B" only version seems to have USB Ports + the optional drive bays over the standard.There are rev B version of the 825:
I was able to position the remaining 8 standoffs for the Gigabyte MZ71-CE0 without any issues - Which is not surprising, because SSI EEB exists since forever.Looks like a few boards do have it there, though it's not consistent. Not used in ATX and smaller and some proprietary Supermicro boards have different placement too. The photos you've posted look to be very old however as if my eyes are not mistaken, they have socket 771 mounts.
Yeah, I'll probably 3D-print something...I believe that historically the dual CPU versions of the X9 motherboards were the ones that required a "revision M" chassis to support the specific standoff that you identify. To get around the issue I've used appropriately sized M3 plastic female-female standoffs attached to the motherboard prior to installation in the chassis.