The settlement of Madagascar came about because of an Austronesian migration from Southeast Asia. The eventual discovery of the island by Swahili, Somali, or other East African traders would be likely, but not inevitable. Butterfly away the
Dayak migration and the island would've remained uninhabited until it was discovered by either Africans, Arabs, or Europeans. Then, if you have an African, European, or Arab attempt at colonizing it that ends in disaster, that might postpone a permanent colonization for quite some time (Europeans were already investigating that part of the Indian Ocean by 1507, but if the first few settlements fail disastrously then it might be postponed until the mid-1600s or even later).