My understanding is that the government could compel Facebook to publish a version of WhatsApp with a special mode that sends all messages to the police if the user ID is 1234567. This introduces a vulnerability but it is limited to one specific person. If your user ID is not 1234567, you're completely unaffected.
However my understanding is that the government cannot compel Facebook to compel a version of WhatsApp that, when it receives a special message, silently starts sending plaintext copies of every other message it receives to the police. Such a mechanism would be a systematic weakness that affects people other than those for which a warrant has been issued, so the notice would "have no effect".
The government could also not compel a source-available app with verifiable builds to stop distributing them so that it can add a secret user ID branch like the one I mentioned above for WhatsApp.
[0]: https://classic.austlii.edu.au/au/legis/cth/consol_act/ta199...
[1]: https://classic.austlii.edu.au/au/legis/cth/consol_act/ta199...