I had this thought last gen and discussed it in a topic on another forum... It got rosted. I do like the idea though. That the /Rock typing on some fossils is because of the fossilization and not their true typing. At least not for all.
Funny...I had this idea last Gen as well and a couple other users (one of them an paleontologist) and me had a lot of fun with the concept... though I didn't call them "Modern Form Kabuto" but "Primeval Form" (I didn't play ORAS so it didn't occur to me that it might sound too much like Primal FormKyogre) or "Original Form"
Let's see if I remember our ideas:
Never had a good idea for Origin Form Kabuto/Kabutops...
Original Omanyte/Omastar: Pure Water -> Water Steel. Original Omanyte and Omastar have the shell curl over the heads and forwards, like modern reconstructions of ammonites. Omastar also has more/longer tentacles and that fleshy thing over the eyes.
Original Aeordactyl: Flying/Rock with rock spikes similar to Mega Aerodactyl
Original Lileep/Cradily: Grass/Water
Original Anorith and Armaldo: Bug/Water (That was before Alola where we got two excellent water/bug lines, but I still think it makes most sense for them)
Original Cranidos/Rampardos: Pure Fighting or Rock/Fighting.
Original Shieldon/Blastiodon: Pure Steel
Original Archen/Archeops: Either Fighting/Flying or boring Normal/Flying.
Original Tirtouga/Carracosta: Previously I couldn't figure out anything better than Water/Rock...but now I'm thinking Water->Water/Fire with a volcano in Carracosta's shell
Original Amaura/Aurorus: Ice/Fairy (due to the gemstones)
Original Tyrunt/Tyranitar: Dragon/Dark (due to it being very very mean/aggressive)
They could put them into something like a Jurassic Park or Marvel's Savage Land.
Also anybody have a good idea for Original kabuto/Kabutops?