It's because certain names and events recur. From our perspective, the mantras found in Samhitas of the Vedas discuss how our Indra, known as Purandara, defeated a demon named Vritrasura in the present Vaivasvata Manvantara, and how Vishnu incarnated as Vamana, the little brother of the present Indra, and defeated an Asura named Mahabali. And certainly when we chant (say) Rig Veda mantras in a Yagna, those Vaivasvata Manvantara events are exactly what we should be thinking of.
But the Vedas are broader than that. As described in the text of the question, the mantras found in the Samhitas of the Vedas are timeless eternal truths that are constantly reverberating in the Universe. And they make reference not just to individual people, but rather to certain roles that are played by different people in different ages. Here is what Adi Shankaracharya says in his commentary on the Brahma Sutras:
Similarly, although individual gods are admitted to originate, there arises no contradiction in the case of such words as Vasu, and the like, since the species denoted by them are eternal. And that the gods, and so on, belong to different species, is to be concluded from the descriptions of their various personal appearance, such as given in the mantras, arthavâdas, &c. Terms such as 'Indra' rest on the connexion (of some particular being) with some particular place, analogously to terms such as 'army-leader;' hence, whoever occupies that particular place is called by that particular name.
And later on he quotes some Smriti text which makes the same point:
Whatever were the names of the rishis and their powers to see the Vedas, the same the Unborn one again gives to them when they are produced afresh at the end of the night (the mahâpralaya). As the various signs of the seasons return in succession in their due time, thus the same beings again appear in the different yugas. And of whatever individuality the gods of the past ages were, equal to them are the present gods in name and form.
So when the Vedas speak of Indra defeating Vritra, they are not just speaking of our Indra but of all the Indras who each confront a demon called Vritrasura. And when they speak of Vishnu taking three steps of land, they're not just talking about Vishnu's present Vamana incarnation, but about all of his Vamana incarnations. And indeed, in my question here I found out about at least two other Vamana incarnations that have taken place in the present Kalpa.
By the way, in this answer I'm giving the viewpoint of the Vedanta school, which is the school of philosophy followed by almost all Hindus today as I discuss here. But there used to be another school of philosophy called the Purva Mimamsa school, and they believed that there are absolutely no names of human beings in the Vedas at all! I think that's patently false, but see my question here for their viewpoint.