There seems to be somewhat a consensus among effective altruists that the Rare Earth explanation is the most likely resolution to the Fermi Paradox. I tend to agree, but like you, I think that effective altruists generally underestimate the risk from aliens.
However, I would caution against a few assumptions that you made in the article. The first is the assumption that aliens would be anything like they show in the movies—rouge civilizations restricted to quadrants in the galaxy. As many have pointed out in the past, a civilization with artificial superintelligence would likely be able to colonize the entire galaxy within just a few million years, which means that if aliens with advanced artificial intelligence existed, we probably would have seen evidence of them existing already. Of course, maybe they’re hiding, but now you’re running up against Occam’s razor.
The second assumption is that we can affect the state of affairs of civilizations at our stage of development. Now, even given the generous assumption that we have the ability to share useful knowledge with aliens at our stage of development, it would be unlikely that we ever find aliens that are exactly at our development stage. A civilization just decades younger would be unavailable to contact without radio, and a civilization just centuries more advanced would probably have artificial intelligence already.