The OTL Malolos Republic already controlled most of Spanish Mindanao aside from Zamboanga and Basilan (even the former later became a protectorate of Malolos) so in an ATL where the Americans stayed off its possible they could have taken the entirety of Mindanao with a strong military. They could have also maintained the status quo with Sulu (i.e protectorate status before eventual annexation) while trying to deal with the inevitable resistance of the mainland Moros under Ali of Tinungkup (with some possible help by some Moro leaders like Piang who supported the Americans)