All the father issues in the ARG tie back to the father issues in Tankmen, primarily Skittles shooting a Tankified Bill in the face.The goo that keeps getting mentioned is actually the darkness that Tankmen are encased in, as seen in this image by JohnnyUtah, as well as for a split second in Tankmen 0.5 before a newly converted Bill puts his helmet on.
The AI's connection to the goo is probably an attempt to bring the first Tankman super-soldier to life without a human host, but that just ended up as a monochrome blob (similar to but canonically not the same as the mod's Bob), so Lennon offered himself to become part of the Tankman forces... and his wife and daughter too. Heck, maybe Little Man is meant to represent Lennon, as said above.
Overall, it seems like the entire Bob mod is nothing more than another cryptic clue in the ARG all about the mascot of Newgrounds itself... which is also why it's a mod for Friday Night Funkin' in the first place.
BUT HEY! THAT'S JUST A THEORY! A GAAAAAME THEORY!