What I meant was....the formation of Malaysia is as OTL, but Sabah (definitely and probably) Sarawak would decided to gain their own independence as a result of the much more messier aftermath post-1969 election...especially considering IOTL, Datu Mustapha, the Sabah Chief Minister during the early 1970s was contemplating to secede from Malaysia, partly due to his opposition of the reduction of state revenue due to the aforementioned Petroleum Act... perhaps as a result of the slightly different goverment post ITTL 1969 election..., instead of deciding to form a party to counteract Datu Mustapha...Kuala Lumpur (for one reason or another) decided to give up and does to Sabah what they had done to Singapore(, which is to kick them out).
As for the Cobbold Commission, considering the rather restrictive nature of the selection of the observers (which had to only consist of the local or Commonwealth members IIRC) perhaps what one way for the scenario you have given to occur is for the Phillipines to decided pursue it claims it at the very least a few months prior to the Commission or.... heck, even perhaps during Magsaysay second term, instead of IOTL where they only decided to pursue it once the commission had already finished, while at the very same time, ask its officials to influence (the actually inexperienced) Lord Cobbold to consider the Phillipines views...