RESPONSE - I agree, and I think this problem extends to a lot of fictional media. There is this tendency to want to create connections for the sake of driving the plot forward, but it often diminishes the larger world-building.
Star Wars immediately jumps to mind. In both the original trilogy and the latest one, there was a lot of focus on lineage. As cool as these twists were, it flattened the world for me a bit. Not everyone needs a space wizard in their family tree.
I understand that there are practical reasons to make the universe smaller in your story, especially in Mr. Robot where focusing on the Deus group would have involved the introduction of dozens of new characters. They used Whiterose as a focus point because they didn't have the time to do all that set up, but like you said, it still made everything feel smaller for me.