My point was that our human body doesn't work by rhetorical reasoning or intuition. There are often things we discover about our immune system that are counter intuitive - for e.g. Using specially developed & formulated vaccines to teach the body to suppress immune response towards antigens (via Treg cells), rather than to neutralize them which is what most vaccines aim to do.

Specifically I was objecting to "Given X, we wouldn't expect Y to happen" aspect of your argument. Its never so simple with the human body! It works in many other domains, and so as a former programmer myself I have to catch myself trying to apply such reasoning to biological systems which can't be modeled like that.