It’s purely my opinion but the article is implying that the McCanns have been cleared from any involvement of MM’s disappearance hence the need to apologise. Other than complete certainty that CB is the culprit, how can they feel it necessary to apologise?
“Portuguese police now say their initial investigation into Madeleine's disappearance was not handled properly, there was insufficient importance given at the time to missing children and that her parents' position as foreigners in an environment they did not understand was not appreciated.”
It's possible they are basically closing the case on their side. Killer's been found. He's out of jurisdiction. Mistakes were made by people who don't work at PJ anymore. etc