From Wikipedia:
If $F, G$ are partial functions on the natural numbers, the notation $F\simeq G$ indicates that, for each $n$, either $F(n)$ and $G(n)$ are both defined and equal, or are both undefined.
What is the difference between this and $F = G$? If $F, G$ take on exactly the same values for each $n$ on which they are both defined, and both are defined for the same values, they are effectively the same from a set theory perspective; this is,
$$ (n, F(n)) \in F \iff (n, G(n)) \in G $$
What am I missing?
You are right. According to what is currently written on Wikipedia's page, writing $F = G$ or $F \simeq G$ has exactly the same meaning, so there is no need for introducing the notation $\simeq$.
But it makes sense (and is very convenient when you are dealing with partial functions) to introduce a special notation, say $\simeq$, to talk about partial function equality pointwise (see here). More precisely, given two partial functions $F, G \colon \mathbb{N}^k \rightharpoonup \mathbb{N}$ and $(n_1, \dots, n_k) \in \mathbb{N}^k$, the notation $F(n_1, \dots, n_k) \simeq G(n_1, \dots, n_k)$ means that
either both $F$ and $G$ are defined in $(n_1, \dots, n_k)$ and $F(n_1, \dots, n_k) = G(n_1, \dots, n_k)$,
or neither $F$ nor $G$ are defined in $(n_1, \dots, n_k)$.
Note that this is completely different from the meaning of the notation $\simeq$ on Wikipedia's page. It turns out that, given two partial functions $F, G \colon \mathbb{N}^k \rightharpoonup \mathbb{N}$, we have $F = G$ if and only if $F(n_1, \dots, n_k) \simeq G(n_1, \dots, n_k)$ for all $(n_1, \dots, n_k) \in \mathbb{N}^k$.
In my opinion, it would be beneficial to modify the meaning of the notation $\simeq$ on Wikipedia's page, in accordance with Occam's razor principle: what's the point of adding a new notation when the ones that are already defined do the same job.