Something I just realized:
Since Mata Nui observed life and cultures on many planets in the outside universe, wouldn't it stand to reason that some of the planets he observed were the ones seen in Hero Factory?
During 2013, while the Lego Message Boards was active, he claim that both universe are not connected:
I only found this text from this archive.
No, there's no connection. HF story team vetoed that right off. At that point, BIONICLE sets were not selling well so they saw no reason to connect the new franchise to the old one.