Re: Sphere Builders' native time period?
You can disregard the novel since it doesn't qualify as "canon".
I've presumed the Sphere Builders (not sure why they're never given a more precise name) were from the future and are trying to prevent their destruction. But since they're always seen against a white background when in their realm, they may be some sort of trans-dimensional beings like the Prophets.
Dr. Howard, Dr. Fine, Dr. Howard: For duty and humanity! --Men in Black (1934)