It's hard to unequivocally prove that gunung padang was man-made at this point, but the refutations of this article specifically are at least as shaky.
At least the archaeologists have soil samples.
It doesn't look like anybody is refuting that the soil samples are that old, the argument against the soil samples are that rocks might have rolled downhill...to the top of this mountain...and corrupted the soil evidence.
The other main argument is that there's no evidence people lived there before.
But gobleki tepe is definitely man-made, ignored for decades after its discovery, and already confirmed to be at least 12,000 years old before half of its excavation has been completed.
We definitely haven't discovered all the man-made megalithic sites.
Frickin Angkor wat went "undiscovered" for centuries until a white guy finally admitted there was an ancient palace sitting right outside siam reap Cambodia that no one believed the locals about.