Amazing claims are fine in the pulpit. You expect to hear them any time in a cathedral. But not at a royal commission.

George Pell was being asked to explain how his absolute conviction that John Ellis was abused as a boy by Father Aidan Duggan – a belief based on a five-month investigation by a church assessor – squared with the instructions he gave to contest the abuse in the New South Wales supreme court.

His claim: to dispute is not to deny. “I made it quite clear to the lawyers that we could not deny that an offence had taken place,” he explained. All they did in court was dispute Ellis’s claims, “put the plaintiff to proof”.

So Ellis was cross-examined for four days about the most private details of his life: the abuse, his marriage breakdown and his sacking by the law firm Baker & McKenzie.

Would it feel any different to Ellis whether his abuse was denied or disputed, wondered the commissioner, Justice Peter McClellan. “We were dealing with Mr Ellis as a senior and brilliant lawyer,” replied the cardinal. “I think he, as a lawyer, would have understood the distinction.”

It seemed lost on McClellan. It wasn’t winning hearts and minds in the gallery. But Pell insisted on the distinction all day, citing as authority the church’s lawyers, Corrs Chambers Westgarth.“It was explained to me … I was not violating my obligation to truthfulness.”

“Cardinal, Corrs weren't your moral advisers, were they?” asked Gail Furness SC, counsel assisting the commission. “No.”

Pell has a way of suggesting tough questions are irrelevant. He is always moving on: “My understandings have matured and improved.” It's clear to him now Ellis should not have been questioned as he was: “The length of the cross-examination was quite inappropriate.”

The cardinal is learning a thing or two about tough days in the box. He’s now had two. Not that he is being quizzed about his private life. Nothing like that. But no one on earth could enjoy what he is going through.

He began the day with little elan and ended with weary resolution. That might be said of nearly everyone in the room. The one figure of inexhaustible energy was Furness, asking her questions with terrifying patience.

Mystery was the cardinal’s word of the day. The biggest mystery to him is a long email written by his private secretary, Dr Michael Casey, which, on a plain reading, has the cardinal trying find a way to disown the church’s own conclusions about Ellis’s abuse.

“This appears to be a contrivance so as to give the lawyers a capacity to argue that the allegations of Mr Ellis should be disputed,” said McClellan. Pell assured the commissioner that was the last thing on his mind. So what was his private secretary getting at? “It’s a mystery to me.”

Pell has his diary with him. In one or two tight spots he was able to tell the royal commission he was in Rome at the time. It was not impressive. But it was a reminder that he will soon be there and raises one question that will never be asked at the commission: is his testimony an impressive curtain-raiser to the cardinal’s new career as the custodian of the Vatican’s finances?

Without doubt.

Pell is absolutely frank that he fought Ellis to protect the wealth of the church. He concedes he fought too hard and the litigation caused the damaged Ellis further harm. He wouldn’t do it the same way today.

But he doesn’t quarrel with the outcome. “One of the few consolations – if that's what I've got – from this sorry mess is that the court of appeal unanimously endorsed the view that the trustees were not responsible in this case.”

No responsibility for the abuse means no payment to victims. That’s how the law has always worked. It so mystified Pell that Ellis and his lawyers argued otherwise that he thought: “We’re not really dealing with entirely reasonable people.”

He has half a day more in the box and then a quick change of costume for the mighty mass at St Mary’s Cathedral with choirs and trumpets to celebrate his departure. Rome will no doubt greet him with the honours due to one who has put his reputation on the line to preserve the patrimony of the church.