Proof of the contrapositive isn’t really a special case of proof by contradiction. Although in both we prove a statement that is logically equivalent to the desired statement and then appeal to that logical equivalence, the two kinds of argument have different structures. When we prove $p\to q$ by contraposition, we prove the logically equivalent statement $\neg q\to\neg p$. When we prove it by contradiction, we prove the very different statement $p\land\neg q\to\bot$; that is, we assume $p$ and $\neg q$ and derive a contradiction.
They do have in common that in both we assume $\neg q$; the difference is that in one we then prove $\neg p$ directly, while in the other we show that further assuming $p$ leads to a contradiction. The notion that proof by contraposition is a special case of proof by contradiction probably arises from the fact that proofs by contraposition can be presented in the form of proofs by contradiction: one assumes $p$ and $\neg q$, derives $\neg p$ from $\neg q$ without making any use of $p$, and argues that the contradiction $p\land\neg p$ shows that $q$ must have been true after all. This is technically a proof by contradiction, but organizing it as such was completely unnecessary: the guts of it was a direct proof of the contrapositive $\neg q\to\neg p$.
On a final note, $\forall x\in A\,\big(\neg Q(x)\to\neg P(x)\big)$ isn’t really the contrapositive of $\forall x\in A\,\big(P(x)\to Q(x)\big)$: the latter isn’t an implication and doesn’t have a contrapositive. You’ve simply replaced part of the formula by the contrapositive of that part, and since it is logically equivalent, no harm has been done. However, there is no reason to expect the result to look much like the result of negating the quantified expression.