Honestly, a lot of the weirdness behind the Bohrok (and a lot of older concepts in BIONICLE tbh) is a consequence of the lore constantly evolving. While the twist about Mata Nui was planned since the very beginning, the precise details surrounding it were not and were constantly being revised behind the scenes. It’s like slowly building a puzzle but the pieces keep changing shape and older ones no longer fit.
Like the Bohrok were always planned to be related to the matoran but not how. One of the original ideas is that they shared a common ancestor but evolved in different directions. Why do bohrok have krana? Because it’s their counterpart to kanohi. Why do they have elemental powers (before air was changed to acid)? Because so do the Toa and their tribes.
Why does the Great Spirit need bugs to clean his face when he’s powerful enough to move planets? Because his backstory was only hammered out years later.
BIONICLE is like a masterpiece that’s held together by scotch tape and elmer’s glue.