Magic can be natural, supernatural, or neither. It simply is. It’s magic. Different scenarios attempt to explain it, but in this case, it seems some of the more overtly supernatural elements have been toned down. Instead, the "magic" appears to stem from a natural source, though still fantastical—just one step removed from the mystical, maybe.
Not to dive too deep, but it’s a bit like how gemstones are believed to possess both natural and supernatural properties, depending on one's interpretation, beliefs, or cultural context. Or how a “magical” hot spring might be viewed—curative and mysterious, yet scientifically explainable. The idea of a diabolical natural phenomenon could still be in play, which would give some weight back to that eerie, supernatural undertone.
As for the backstory—still as clear as mud. The only thing we know for certain is that the mine is no longer abandoned.