I like to believe that the Rock type in fossils represents the fact that they were petrified at some point and haven't been totally "resurected" from that state. In the case of galarian fossils, I'd argue that they managed to create technology capable of actually resurect those pokémon but just partially, which explains why they need two fossils to create one pokémon.
Now going, to the question at hand.
I'd say Omanyte might've been Rock/Water type because of its shell and losing it be the reason why Octillery is a pure Water type with a really strong head. I'm ignoring completely the fact that Johto's dex says Omastar stole its shell from Shellder because that's more of a theory really and the fact that it only appears in one entry is kinda sus not to mention its shell doesn't look like Shellder at all and it's also not heavy enough to later say Omastar went extinct because its shell became too heavy for it.
Kabuto might as well be a Bug/Water type. It's based on a trilobite and a horseshoe crab, the latter being apparently closely related to the extinct eurypterids (sea scorpions). Horseshoe crabs belong to the Chelicerata subphylum, which includes arachnids, often represented as bugs in this franchise.
Aerodactyl I'll say could either have been a pure Flying Type or Rock/Flying. As much sense the dragon typing would make, it doesn't learn any dragon attacks naturally, so it wouldn't make much sense for it to be a Dragon type imo. It also has the ability Rock Head and is given to Rock type pokémon only, with a few exceptions.
Anorith could've been a Water/Bug, given how it used to live in the sea. However, Armaldo might've been a Fighting/Bug since it becomes unable to survive in the water and given how its armor made it possible for it to punch through steel plates. It could also have only lost its Water type and become pure Bug, considering how it doesn't learn any fighting moves naturally either.
Cradily's Dex entries suggest it might've been a Water/Grass pokémon.
Shieldon could've been Rock/Steel or simply Steel typed. Both Shieldon and Bastiodon's Dex entries focus on the same exact things, so there's not much to work with.
Cranidos was a Rock-type.
Tirtouga could've been either Water/Steel or simply Water type. Its PokéDex entries focus on how strong their teeth are, saying they could break even steel beems and bones from their prey. It also says Carracosta uses those bones to craft its shell, contrary to Omastar that apparently grew with it. Some of Carracosta's Dex entries also say how it could've been the ancestor of many turtle pokémon, and these pokemon shells never affect their typing with the possible exception of Drednaw that only gets that type after evolution.
Archen is just a bird haha. It probably was simply a Normal/Flying type like any other bird pokémon, even its PokéDex entries suggest it might've been an ancestor to those.
Tyrunt might've been simply a Dragon type. I don't discard the possibility of Dragon/Rock typing for Tyrantrum, but it just learns Head Smash and Rock Slide naturally. Head Smash is just a really strong headbutt and Rock Slide is learnt by many non-rock type pokémon with a lot of physical strength, and while Rock Head is a possible ability, it's a hidden ability, unlike Aerodactyl. Dark/Dragon also fit because of its selfish personality
Amaura's entries suggest it was a pure ice-type. Like with Shieldon, Amaura and Aurorus entries, both focus on pretty much the same thing so there's not much to work with.
