Caves are an interesting one... they're the 'birthplace' of human culture (cave paintings and so on), so despite their grim bleakness, they have a certain 'homely' quality. They afford shelter and warmth, but can also be fraught with dangers of their own. The Biblical cave is a place of 'rebirth'. Lucretia's cave in FFVII is quite the opposite; she hides there, unable to die and haunted by terrible dreams. Materia caves are places where the Lifestream, and the knowledge within it, are 'reborn' into the world... yet as Bugenhagen says, the formation of Materia detracts from the Planet's own life.

The cave in Wutai doesn't cast any spells... it's just inhabited by supernatural fires, much like the cave behind Cosmo Canyon is inhabited by the undying souls of the Gi.

You could say that FFVII's caves are symbols of 'undeath' rather than the rebirth of life...

or you could say that this kind of religious comparison is simply reading far too much into a game's usage of natural phenomena.