According to the official ruling for Mimic Vat, you choose a card to make a copy of in case if there are multiple cards exiled with Vat's first ability (e.g., melded permanent died).
According to the official ruling for Panharmonicon, Prototype Portal would create a token for each card, exiled with it's first ability when it's second ability is activated.
It seems like rule 607.3 equates phrases “the exiled card” and "a card exiled with ":

If, within a pair of linked abilities, one ability refers to a single object as “the exiled card,” "a card exiled with ," or a similar phrase, and the other ability has exiled multiple cards (usually because it was copied), the ability refers to each of the exiled cards.

So, what does the rule actually mean? Are this phrases equal and ruling for one of the cards is wrong? Or are they different, and I missed the difference?
Edit: card tags

Edited Kirill Afonin (Oct. 28, 2018 11:27:54 AM)