I don't think it's ever correct to define $\bigcap \emptyset=\emptyset$. One always expects that taking an intersection of more things should get you a smaller result. (The set of big red ugly expensive things is a subset of the set of big things.) That is, $$\def\S{\mathscr S}\text{if $\S\subset \mathscr T$ then $\bigcap \mathscr T\subset \bigcap \S$}.$$ But having $\bigcap\emptyset = \emptyset$ would spoil that. So that answers one of your questions, which is why we don't do that. I find it hard to believe that any serious text for set theory would do as you say and make $\bigcap \emptyset = \emptyset$.
In set theories with a universal set $V$, one takes $\bigcap \emptyset= V$ for that reason; then we have $\emptyset\subset \S$ for all $\S$ and also $\bigcap \S \subset \bigcap \emptyset = V$, as we would hope. In set theories without a universal set, most notably ZF, one leaves $\bigcap \emptyset$ undefined.
In ZF there is no axiom of intersection that corresponds to the axiom of union; one uses the specification axioms to define intersections. Recall that this means that for any predicate $\Phi(x)$ and any set $X$ we can construct $\{x\in X\mid \Phi(x)\}$, the subset of $X$ for which $\Phi$ holds. Let's see how this goes in this case. We want to take the set of all $s$ that are in every $S$ that is an element of $\S$. But to use the specification axiom schema, we can't take this condition by itself; we have to attach it to some set $X$ and use it to select the desired subset of $X$.
So in ZF the best we can do is $$\{x\in X\mid \forall S\in \S . x\in S\}$$ for some set $X$, which we might agree to abbreviate as $$\def\S{\mathscr S}\bigcap_{(X)}\S.$$ This is the subset of $X$ whose elements are in every element of $\S$, or we might call it the intersection of $S$ "taken relative to $X$". If there were a universal set $V$ then we could take the intersection relative to $V$ and be done (and note that then $\bigcap_{(V)}\emptyset = V$) but ZF has no universal set.
But it should be clear (or you can take it as an exercise) that no matter what $X$ is, if $S\in \S$, we have $$\bigcap_{(X)}\S \subset \bigcap_{(S)} \S.$$ From this it immediately follows that for any $S, S'\in \S$, then $$\bigcap_{(S)}\S = \bigcap_{(S')}\S$$ so it doesn't matter which element of $\S$ we take the intersection relative to.
This shows that when $\S$ is nonempty, there is a unique maximal relative intersection of the elements of $S$, which we can abbreviate as simply $\bigcap \S$. And since $$\bigcap_{(X)}\S = X\cap \bigcap \S$$ the relative intersections weren't getting us anything interesting, and we lose nothing to forget about them. In particular it doesn't matter if we take $X = \bigcup \S$ as you suggest, because the intersection is the same regardless. So we may as well take the simpler definition.
On the other hand, when $\S=\emptyset$, we have $\bigcap_{(X)} \S = X$, which is rather useless, so we lose nothing to forget about it.