are you talking the positioning screws that go through the back of the dropouts, or the plates that seem to take up the space normally filled by a claw mount derailer?
the screws area well explained above, the plates seem to be intended simply to avoid positioning errors on the assembly line. With the plate installed, there would be no reason to reset any jigs used during assembly. Most of them I've seen have been on bikes built when direct mount derailers were starting to take over. Some bikes have chainside dropouts that are only half as deep for the same reason.
Strangely, I hadn't seen any in years, then two bikes I bought last week both have them
Not critical if you are carefull when installing the wheel.
Ken.