I reassembled a Mac Pro A1186 and have extra parts left over. What do they go to?
I'm posting this as a pure guess, just so I can add a picture...

The underside of the drive bay has a lot of screws like the ones in your picture, &amp; also the pic shows one of many areas, under the PSU housing, that uses that type of 'spacer' as sliding locks - just in case they're not actually spacers.
Picture is from the Mac Pro 3,1 Service source - the yellow-circled screws are from the PSU &amp; are dome-heads. The ones similar to your pic, button-heads, are the non-circled screws.  

The red-circled area is what I meant for the 'spacers' - drive locks perhaps, activated by the release handle at the back of the Mac [I've 3 different Pros here, but all are in use so I can't take them apart to check ;)

I've never taken the mobo out of a Mac Pro, so never seen underneath to know what the spacers may look like.