I called the Ministry of Foreign affairs on the number they have on the Acknowledgment of Receipt for the certificate application.
And the person I spoke to had some difficulty speaking in English, however, she did confirm that it's ready for collection and said; if it is approved, it should be available for collection.
I will call the embassy tomorrow and ask them too. Because I don't think it's ready for collection just in Malaysia. And I also don't think they send it to the Malaysian Embassy here in Canada. If approved, the certificate is actually issued at the embassy. That's my guess. But you should call the embassy tomorrow too and inquire.