In the first case you are right. But a quick scan around the official documents does not provide proof for that. Have you seen an official document?
In the second case we stay with 1 location. The 11 locations of the churches would then be points of interest, a further future project next to the official locations as suggested before by nfmungard.
I have no proof that it could belong to the first case.
Maybe we are in the second situation, as for the Boyne Valley (3 separate places in a central area), so I think the future project next to the official places is a good idea.
It could also highlight major places in historic centers (eg the Eiffel Tower). For example, the Kremlin and the Red Square seem to me to be 2 distinct locations; just like the Puys chain and the Limagne fault. There are plenty of examples.