The answer you link to answers this question, at least implicitly. But since you've already read that, perhaps a rephrasing will help.
Gödel defined a subclass of the universe, the so-called constructible sets. This is denoted $L$. He also showed how to construct a functional formula mapping the class of all ordinals 1-1 onto $L$. It's easy enough to restrict this so that we have a 1-1 correspondence, defined by a formula, between the constructible reals and an ordinal. Or equivalently, there is a definable well-ordering of the reals.
So if $V=L$, i.e., all sets are constructible, then there is a definable well-ordering of the reals. Gödel showed that it is consistent with ZF to assume that $V=L$. (This was the basis of his famous pair of results that Con(ZF) $\Rightarrow$ Con(ZFC) and Con(ZFC+GCH).)
Therefore we cannot prove in ZF (or even in ZFC) that there isn't a definable well-ordering of the reals.
On the other hand, Cohen constructed a model of ZFC in which there is a non-constructible real. It turns out that in this model, there is no definable well-ordering of the reals. So we cannot prove that there is such a definable well-ordering.
As you point out, asking if there is a definable well-ordering of $\mathbb{R}$ is equivalent to asking if there is a definable bijection between the $\mathfrak{c}$ and $\mathbb{R}$.
Summing up, we have a candidate formula, but we can't prove it does or doesn't do the job.
Turning to the Axiom (Schema) of Replacement, this allows one to use parameters. (All my mentions of "definable" above should be read as, "definable without parameters".)
That is, the functional formula $\phi$ that occurs in it
is $\phi(x,y,w_1,\ldots,w_n)$. If we have some function $f$ (i.e., a set of ordered pairs satisfying the usual functionality constraint), that can be one of the parameters $w_i$, even if we have no formula defining $f$.
So any function can be used in Replacement, provided that the function is a set of ordered pairs, and not a proper class.