Something you always have to keep in mind with Bionicle is that a lot of story details were retconned, and the earliest versions of the story tend to have much better possible explanations for a lot of the stuff in 2001 and early 2002.
So let’s take a look at what the early story material has to say:
In “The End of the Toa?” on page 7, there’s this bit of dialogue as the Toa are about to fall down the tubes:
Onua: “Looks like Cahdok and Cahdok had one more surprise for us!”
Lewa: “This is not their doing! this comes from the very heart of Mata Nui.”
Consider also the Nuva symbols that suddenly pop out of the suvas. I think perhaps the implication is that those were always there, but had simply now been unlocked.
In the early versions of the story, the Mata Nui robot was an evacuation vehicle containing the survivors of a dying planet, lying in suspended animation for the duration of the voyage. I suspect that Papu and Rangi (the original Great Beings?) were the only ones who weren’t asleep, though I’m guessing they must have been trapped somewhere (the Red Star mothership?), only being able to help the Toa’s quest indirectly by remotely activating various systems on Mata Nui that Makuta had not yet gained control of.
If I had to guess, I’d say the original intent was that the transformation chambers were created by Mata Nui and/or Papu/Rangi during Mata Nui’s voyage, and the Toa were about to receive those upgrades when Makuta sabotaged the GSR. This would explain why the suvas had the Nuva symbols and why the transformation chambers exist in the first place.
Perhaps it was Papu and Rangi who remotely activated the transformation chambers once the Toa defeated the Bahrag. Opening the chambers too early might have allowed the Bahrag to use them on the Bohrok, which would be bad news for the Toa.
Also, don’t forget that the Bohrok-Kal were a last minute addition to the story so LEGO could stall for time while the Mask of Light movie/story was developed. So you can just pretend they don’t exist. I wonder if the Rahkshi would have been the ones to steal the Nuva symbols originally…
I think trying to make sense of any of the mysterious stuff from 2001-2003 in the context of the final canon is futile. The story had already been massively altered by 2004, and by 2006 it was almost unrecognizable.