Let $A$ be a commutative ring with $1 \neq 0$. Then writing $V(1) = V((1))$, we have $\bigcap_{\mathfrak{p} \in V(1)}\mathfrak{p} = \sqrt{(1)} = (1)$.
But then $\bigcap_{\mathfrak{p} \in V(1)}\mathfrak{p} = \{x : x \in \mathfrak{p} \text{ for all prime ideals } \mathfrak{p} \supseteq (1)\} \supseteq \text{Set}$, where the last containment is justified since there is no prime ideal that contains $(1) = A$, so $x$ can be anything by vacuous truth.
I had a similar confusion like this in my topology course, but the answer that I heard from my teacher was that "of course, $A$ is the universe that we consider," so $\bigcap_{\mathfrak{p} \in V(1)}\mathfrak{p} = \{x \in A : x \in \mathfrak{p} \text{ for all prime ideals } \mathfrak{p} \supseteq (1)\} = (1)$.
But then why "pure" definition from (naive) set theory fails and forces us to consider $A$ as the ambient space?