I don’t know what to think but am watching this as a friend has an Evo frame to build up later in the year. It is very odd that the “same” parts are a different size in the frame and that Spec told you to put the smaller one in given your reportings to them.
They are a big old company so if they had a big bad batch they may have been able to get SRAM to help them out. I remember reports that Spec had over sized 05-06 Enduro headtubes and that some people were having issues putting chris king headsets in for this reason. There was even discussion about slightly oversize headsets.
A strange situation here if the parts are the right ones.