240.4(F) clearly says it applies to a delta-delta transformer. It does not allow the primary device to protect the secondary conductors of a delta-wye transformer, regardless if the load is 3-wire only.
As you agree, a L-G fault of only 2PU (using your numbers 2*125A = 250A) on secondary yields only 1.15PU (62.5A) on the primary is not enough to cause the primary device to operate in a timely enough fashion to protect the secondary.
