They speculated that immune systems evolved to avoid being continuously on alert. And that's exactly right- our immune systems have an extremely complicated system for detecting foreign invaders that is tightly regulated. And a failure to regulate that is often associated with autoimmune disorders, which remain very poorly understood.
I've studied biology from the perspective of engineering better drugs for decades now and I can say with confidence that I simply don't understand how the immune system works, and I don't think anybody else really does either (compared to, say, the heart, or many biological systems like protein production). We have identified many players, and observed a great deal of actions, and have speculative models for many of the underlying processes, but we don't really have an "understanding" of the immune system. I skimmed this paper and frankly, it has a very long way to go before people are convinced to try this in human clinical trials.
I look forward to innovations, but to a first order approximation: evolution found model parameters that exceed the best human science and engineering.
You can just stop taking antibiotics and vaccines.
Those are way more interesting odds.
You wouldn't want to get vaccinated for smallpox in the middle of a plague epidemic, because that would waste your immune system's resources on an extinct-in-the-wild disease, when it really needs to be gearing up to stop the plague killing you.
You do not somehow go into deficit by getting a vaccine.
I personally look forward to every innovation that potentially improves our baseline.