Good question!
Indeed it depends on the interpretation of "finite intersection". If we understand a finite intersection as the intersection of $n \ge 1$ sets, then you are right: Willard's definition would require that a subbase $\mathscr C$ covers $X$.
Some authors explicitly require this. For example, in Munkres's "Topology" one finds
Definition. A subbasis $\mathcal S$ for a topology on $X$ is a collection of subsets of $X$ whose union equals $X$. The topology generated by the subbasis $\mathcal S$ is defined to be the collection
$\mathcal T$ of all unions of finite intersections of elements of $\mathcal S$.
However, Willard claims that any collection of subsets of a set $X$ is a subbase for some topology on $X$. This can't be true with the above interpretation of finite intersection. As you say, one must include the empty intersection to make it work.
The concept of an empty intersection is not unproblematic. It only makes sense if we consider a family $\mathscr A$ of subsets of a given set $X$. In fact, we can define $\bigcap^X \mathscr A = \{ x \in X \mid x \in A \text{ for all } A \in \mathscr A \}$. For non-empty $\mathscr A$ this agrees with the usual definition $\bigcap \mathscr A = \{ x \mid x \in A \text{ for all } A \in \mathscr A \}$. However, the definition $\bigcap \emptyset = \{ x \mid x \in A \text{ for all } A \in \emptyset \}$ does not make sense; it would produce the "set" of all objects $x$, and such a thing does not exist. In contrast, $\bigcap^X \emptyset = \{ x \in X \mid x \in A \text{ for all } A \in \emptyset \} = X$.
So we should better call $\bigcap^X \emptyset$ the empty intersection relative to $X$.
Some authors use a completely different definition: They call $\mathscr C$ a subbasis for a topology $\mathscr T$ if $\mathscr T$ is the coarsest topology containing $\mathscr C$. Clearly $\mathscr C$ must contain all finite non-empty intersections of elements of $\mathscr C$ and $X$.
This avoids the above discussion.
Remark.
Munkres discusses the concepts of "empty union" and "empty intersection"on p.12 in the section "Arbitrary Unions and Intersections". For any collection of sets $\mathscr A$ one can define
$$\bigcup \mathscr A = \{ x \mid \text{There exists } A \in \mathscr A \text{ such that } x \in A \} .$$
This also makes sense for $\mathscr A = \emptyset$; we get $\bigcup \emptyset = \emptyset$. Note that this is relevant in Munkres's definition of a subbasis since the empty set belongs to $\mathcal T$.
Concerning $\bigcap \emptyset$ he gives the same arguments as we did above. However, he states
Not all mathematicians follow this convention, however. To avoid
difficulty, we shall nor define the intersection when $\mathscr A$ is empty.