I think you are right. In fact, that hypothesis you just gave: the notion that an indigenous person believed a world destroying flood deposited ancient fossils of sea-creatures in the mountains...that is the explanation given by Jesus Alvarado-Ortega et al when explaining why Mayans would bring fossils of fish into Palenque here.

There's some evidence that indigenous people understood fossils as giant and dead ancient animals. Adrienne Mayor has written two books on the subject, one on fossil use in the Americas, and another about fossil use in the Greco-Roman world, a short summary here. A notable commonality between the New World and the Old, is that peoples in both places viewed these objects as the relics of giant ancient and sometimes ancestral beings, be they human or animal, who lived in primordial times or in a previous creation.

There are even two artistic reconstructions of the pre-fossil animal, done at rock art sites. Perhaps, some Fremont people observed theropod tracks at a site called Cub Creek in Utah, and re-created those giant lizards with much smaller humans in rock art nearby. Perhaps, a San or Bantu person at Mokhali cave in Lesotho, painted an ostrich-like reconstruction of an orithopod and its track; as orithopod tracks are found in the region and there's a fossil skeleton in the cave wall. I've written about the many examples of North American fossil-use here, and I love the other two answers about other aspects of ancient fossil use.

You asked as well, why are deluge floods spread around the world? That is of course a difficult question to answer. The easiest explanation is that it has a certain relevance and power when used in oral societies which allowed it to be conserved across long time and geographic scales. It is one of many trans-cultural myths cataloged recently by Jean-Loic Le Quellec and Bernard Sergent, in "Dictionnaire critique de mythologie"; which sadly has no english version yet.

So far, Jean-Loic has mentioned that they've collected 551 examples of world-wide flood myths; including in Africa and including many in-land (saying that it's not a particularly coastal phenomenon). It is the idea of Jean-Loic and Julien d'Huy that these myths (or at least tropes within the myth) have been conserved from the wider variety of myth during the paleolithic period. So the effectual reason why these myths are world-wide is because they spread with people during our paleolithic migrations. Besides the flood myth, there's many other foundational stories and ideologies that were presumably believed during the paleolithic, basic concepts such as a three-tiered cosmology, basic mythological figures such as upper world avian beings and lower world watery serpent beings, and narratives such as the cosmic hunt, the deluge, and others.

In lieu of buying Jean-Loic's book in French, you can read a related paper here, while I can't find anything uploaded to the internet about the flood myth, this paper references flood myths as it's on the narrative of a person swallowed by a giant sea-animal. There is much information available about this subject of mythology for reading at your discretion on Jean-Loic Le Quellec's and Julien d'Huy's academia pages.