(Most) vaccines work by letting your immune system know to watch out for particular things. That's an information advantage. Likewise, antibiotics are chemical agents that the body lacks the genes to synthesise. Betting that the immune system's parameters are generally well-calibrated is entirely compatible with taking antibiotics and vaccines, where indicated.
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.
The immune system does expend resources on vaccines: it makes antibodies, usually has some kind of inflammatory response…. But if a vaccine causes a nutritional deficiency, there's something seriously wrong with your diet.