When light clashed with darkness in 2003 in the caves beneath Mata Nui it was marked by these logos and nametags. They had a hint to the bigger story. The fact that they fit together is very in line with Bionicle mythology like the jing-jang logo. Takanuva had to merge with Makuta to defeat him. Light and darkness are connected and Makuta actually did god by securing that only the right heroes reentered the giant robot to restart it. Just like the body actually grows stronger and more immune after a virus.