Or what if there was some form of civilisation before the Okototians, and some kind of horrible event, some form of great cataclysm, wiped them all out.
This is why matoran are small
Maybe they just burrow?
Yeah I dunno
Wait a minute. If the Bohrok came from Av-Matoran, where did the Bohrok-Va and Bohrok-Kal come from?
Bohrok-Va: https://biosector01.com/wiki/Bohrok_Va"The Bohrok Va were created by the Great Beings to assist the Bohrok"
Bohrok-Kal: https://biosector01.com/wiki/Bohrok-Kal"The Bohrok-Kal were created by the twin queens of the Bohrok swarms, Cahdok and Gahdok. The Bahrag exposed six Bohrok, one from each swarm, to a mutagenic substance."
So baisically the Va were created entirely by the great beings, but the Kal were created by the Bahrag's own volition, by exposing regular bohrok to whatever it is the make the Krana with. Neat.