B.C. is not set in prehistoric times, but in a post-apocalyptic second Stone Age.This would explain the anachronisms, such as the fact that all the cavemen are Christians.
B.C. and The Flintstones share a universe.The differences in tone can be explained easily — Bedrock is a respectable-size city for the modern Stone Age. BC is set in a considerably more rural area. After the End. In the case of the latter, it would take place somewhat closer to the Great War than the rest of the series. But hey, this is WMG.
The dinosaurs and other prehistoric creatures that appear in B.C. were cloned ala Jurassic ParkWell, if the comic sets in the future, then the extinct animals should have been resurrected at some point by some way. It may also explain why the Velociraptor that appear in later strips are big and featherless.