Completely acceptable as long as it is disclosed.
We frequently use aftermarket parts if a Toyota version is not in stock and the job needs to be done--especially on older vehicles where parts support is no longer available.
That said, it is the service writer's duty to disclose this and let the customer decide.
I can totally understand if a job needs to be done and OEM part isn't available that they'd use aftermarket.
Are you saying that aftermarket is a last resort or that they use aftermarket over OEM even when both are easily available?