The ultimate point of performance depends upon the availability of the items ordered through the Purchase Order. Initially a Purchased Order is made and the effective date for the items mentioned therein shall be from that date. In case a modification is made and additional items are included, the seller has to make a fresh attempt to procure the items. It is not fair to stick to the previous date of the PO and say it should be performed within the period mentioned therein.
"...As there is a Late supply-related penalty and it is a single consolidated supply..." By this you mean to say that the supplier supplied all the articles ordered in the first order and modified the order together and going by the effective date, the items of the first order were supplied with delay.
It all depends upon how the modification is made and whether any mention is made to supply the items of the first PO first and the items now included with effective date of the modified order. Both documents need to be examined.