The statement is false.
Fix an integer $m \ge 1$ and set $d = m + 1 \ge 2$. Consider the case $k = 2$. We construct a sequence of integers $n \to \infty$ and corresponding sets $S_n \subseteq \{1, \dots, n\}$ satisfying the given conditions, yet having $p_{2,S_n}(n) = 0$.
For any integer $n$ such that $n \ge 1$ and $n \equiv 1 \pmod{d}$, define the set: $$S_n = \{ s \in \{1, \dots, n\} : s \equiv 1 \pmod{d} \}.$$
We can make $n$ arbitrarily large. By definition, $S_n \subseteq \{1, \dots, n\}$. Also, since $n \ge 1$ and $n \equiv 1 \pmod d$, we have $1 \in S_n$. Therefore, $\gcd(S_n) = 1$.
Now we have to show $S_n \cap [x, x+m] \neq \emptyset$ for every integer $x \in \{1, \dots, n\}$. Let $x \in \{1, \dots, n\}$. Let $s$ be the largest element of $S_n$ such that $s \le x$.
If $x=s$, then $s \in S_n \cap [x, x+m]$ since $m \ge 1$.
If $x > s$, let $s'$ be the successor of $s$ in $S_n$. Since $S_n$ consists of elements congruent to $1 \pmod d$, $s'$ exists if $s<n$, and $s' = s+d$. We have $s < x < s' = s+d$. Since $x \ge s+1$, we have $x+m \ge s+1+m = s+d = s'$. Thus, $s' \in (x, x+m]$. This implies $s' \in S_n \cap [x, x+m]$.
If $s=n$ (which implies $x=n$), then $n \in S_n \cap [n, n+m]$.
In all cases, the interval $[x, x+m]$ contains an element of $S_n$.
Now, consider the partition count $p_{2, S_n}(n)$. This is the number of multisets $\{x_1, x_2\}$ such that $$x_1 + x_2 = n, \quad \text{with } x_1, x_2 \in S_n.$$
Since every element $x_i \in S_n$ satisfies $x_i \equiv 1 \pmod{d}$, taking the equation modulo $d$ gives: $$n = x_1 + x_2 \equiv 1 + 1 \equiv 2 \pmod{d}.$$
However, we constructed $S_n$ for integers $n$ such that $n \equiv 1 \pmod{d}$. Combining these congruences gives: $$1 \equiv n \equiv 2 \pmod{d},$$
which implies $d \mid (2-1)$, so $d = 1$. This contradicts our definition $d = m + 1 \ge 2$.
Therefore, there are no solutions to the equation $x_1 + x_2 = n$ with $x_1, x_2 \in S_n$ and so $$p_{2,S_n}(n) = 0.$$
Since this holds for an infinite sequence of $n$ tending to infinity, the claim that $p_{k,S}(n) \ge c n^{k-1}$ for some $c>0$ and all sufficiently large $n$ cannot be true for $k = 2$.