Unown got Psywave back then and Hidden Power afterwards, still two forms of waves, radiations in fact are invisible but can measured and the power varies depending on the element or subject and its level of absorbtion and emittence.
You can perfectly use ancient calamities and compare them with the modern day ones in a single reference including the ruin symbolism, jomon alphabet (most of ancient west alphabets looked similar anyway), people and ainu, basically spiritual and old Japan mixed with modern one.

For example Ho Oh is already based on a Hoo / Fenghuang but is also a phoenix, considering the the beta GS themes it could easily fit the Japanese rebirth theme through its history, either be it natural disasters or civilization conflicts and everything they have brought.

Considering the ammount of Pokemon with two faces / two sides in both beta and final versions and the duality theme in general, I can honestly see it working outside of the pokedex too.

As for the mapping and location design the ruins were clearly meant to be ancient ruins and the beta being a sort of a shrine cave, shrines in Japan are mostly build nearby forests, caves or waterfalls, as proven by the location of all the shrines over Johto and the following regions, but it doesn't mean those cannot be used in the story to rappresent more than one location or event.


Why can't it be both and not mandatory black or white?

Also this:
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAH


https://www.youtube.com/watch?v=_Iem9iN1Ds8

https://www.youtube.com/watch?v=9BVckjdZlK4

https://www.youtube.com/watch?v=iutuQbMAx04

https://www.youtube.com/watch?v=q9x6jYsv91g

https://www.youtube.com/watch?v=ksDpv-xcqjs