Nothing red herring. You know how the immune system learns? By being confronted with bad actors. Too less bad actors, your body becomes the target.

About the gut microbiome: bad bacteria can only take over, if there's a hole in an already established biome or if it's generally weakened. But then that's a huge issue, you're usually in a sterile tent in a hospital, fed intravenously. A baby already has a healthy microbiome.
It's not about the microbiome, it's about the immune system. Think of them as separate entities, even though they are heavily intertwined.

Where do you think both reside?

Gut bacteria: gut

Immune system: gut, veins, mostly bone marrow tho.