Why the restriction on the length of the proof in a $(r,q)$-verifier in PCP is inconsequential?
The formal version of "the limitation on the proof length is inconsequential" is the following:

If $L$ has a $(r(n),q(n))$ PCP verifier, then it also has an $(r(n),q(n))$ verifier with proof length bounded by $q(n)2^{r(n)}$.

The above holds since as you mentioned, the verifier can ask $2^{r(n)}q(n)$ different queries on a length $n$ input ($q(n)$ queries for each possible outcome of the verifier coins). Let $f_x$ be an embedding (one to one mapping) of the possible verifier queries on input $x$ in the set $\{1,2,...,q(|x|)2^{r(|x|)}\}$. Let $V'$ be the verifier who acts like $V$, with the sole difference that when $V$ asks for index $i$, $V'$ requests $f_x(i)$. It is easy to see that $V'$ is a verifier for $L$ with the same properties, and bounded length proofs.