Let $V$ be a finite dimensional vector space and $(v_n)_{n\in J}$ the basis of $V$. By permutation of the order of the basis elements I mean that $Av_n = v_{\sigma(v)}$ for some $\sigma \in S_n$ where $S_n$ is the symmetric group on $n$ letters.
I understand that the question may sound a bit nonsensical: “If $A$ permutes the basis vectors then isn’t it by definition a permutation matrix in the sense of Wikipedia?”. What I mean is that it makes total sense to me that if the basis vectors are standard in the sense that $\pi_i(v_j) = \delta^i_j$ (with projection mapping $\pi$ onto the $j$th coordinate and Kronocker delta), then yes, $A$ must only contain zeroes and ones as per a standard permutation matrix. But what if the basis is not standard, i.e. the condition $\pi_i(v_j) = \delta^i_j$ does not hold? In that case assuming that the permutation property of $A$ holds, what do we know about its structure?
If you multiply any square matrix $A$ by a permutation matrix $P$ of the same size, it's easy to see that the result simply permutes either the rows or columns of $A$, depending on whether you premultiply or postmultiply. So the answer to your question is "yes" whether or not a standard basis is used.