I don't think Singapore would be able to get jack out of the deal, even with the miracle worker that is LEE. Malaya has a better shot, but merging Sabah with Sarawak or Brunei would have been more viable regardless.
As for Indonesia, Sukarno is an ambitious SOB. Just look at what happened in East Timor. His claim there is essentially 'anti-colonialism', which rings very hollow considering he annexed an independent nation shortly after Portugal left. It's the same argument he used IOTL for Konfrontasi against Malaysia. In fact, a fractured Borneo outside Malaya's control would embolden him even more.
As for the Philippines, not too sure. Their claim to Sabah laid with the Sulu sultanate, but the claim can also be a double-edged sword for the Sultanate's pretenders to pry its island territories from Manila's control, maybe even as far as Mindanao is things really go south.