"Had the respondent consulted the employees in accordance with its consultation obligations – such that we could have been satisfied that the decision to introduce the site access requirement was the outcome of a meaningful consultation process – the above considerations would have provided a strong case in favour of a conclusion that the site access requirement was a reasonable direction."

"But in its judgement, the commission said the outcome might have been different if BHP had handled things differently:"
https://www.abc.net.au/news/2021-12-03/bhps-vaccine-mandate-unlawful-fair-work-commission-finds/100673390

According to the judgement it was all about consultation with workers that decided the court's decision.

had BHP consulted with workers "in accordance with its consultation obligations..... would have provided a strong case in favour of a conclusion (that) was a reasonable direction"

so the case was won by CFMEU on a technicality wrt consultation, not because the decisions was illegitimate.

"Had the respondent consulted the employees in accordance with its consultation obligations – such that we could have been satisfied that the decision to introduce the site access requirement was the outcome of a meaningful consultation process – the above considerations would have provided a strong case in favour of a conclusion that the site access requirement was a reasonable direction."