It was not integrity of border control; it was political theater.

AUS government was OK with exceptions set up by AO and Victoria government (as PM said day before), so they instructed ABF to let those few who are coming for AO. That's how Czech player and other person got in.

Then, PM got a wind of public opinion (after Novak stupidly posted on social media that he got exemption) and changed the tune while Novak was in flight. He instructed ABF to detain him. They were hoping that he will comply and just turn around. He was not cooperative, so they kept him for hours in isolation while they were running around like headless chicken, consulting with politicians what to do.

Finally, decision was made to cancel his visa. He asked for a bit of sleep and time till morning to consult with his team and with TA. It seems that people at airport were sympathetic to him, so they agreed, prepared a bed and sent him to sleep.

So, probably someone from government called and found out that they let him sleep till morning. They didn't like that and urged border agent to wake Novak up and deliver notice of cancellation to groggy Djokovic.