The degree to which it helps or not depends on the implementation. For example, free could be a slow path that does extra bookkeeping lookups the sized variants wouldn't need to. Large allocations and non-default aligned allocations often use different bookkeeping data structures from how most allocations are handled internally anyhow. In such cases that check needs to be done up front, and at least on virtual memory systems (where it's relatively easy to segregate allocations types by VM range) it doesn't much matter whether you're indexing that first level directory based on pointer or size.
But, yeah, it's not an ideal situation from the perspective of free_aligned advocates.