Not anything to do with head to intake mismatch I don't think. My Edelbrock Airgap intake was for rectangular port heads, which matched the heads perfectly and I still have the extra holes. Just speculating, but I think it might have to do with a head / intake engine generation mismatch.
Had I dropped that intake onto the cast iron Gen IV 396 heads I had previously, there would have been threaded holes to match. That intake onto more modern aluminum heads with raised exhaust ports? Extra holes. Probably better to have them and not need them than need them and not have them.
1968 Impala SS