The distance between the Mascrene Islands and Madagascar is only a few hundred kilometres, there it is a mystery why the Malagasy did not settle these islands. The POD is sometime during the earlier part of the 2nd millennium AD the Malagasy settle both of these islands. The settlement could have been a totally accidentally one (the migration of people from Borneo to Madagascar could have very well resulted from a fleet being totally blow off course).
In this TL when the Portuguese first visit these islands circa 1500, instead of finding them being uninhabited they find them being inhabited with Malagasy people who practice agriculture based on the growing of Rice. I am not sure on the amount of contact between the Malagasy and these islands and Madagascar. This population is going have a much more complex society than the Khoikhoi, along the lines of the Guanche on the Canary Islands when the Castilian first encountered them.
It is very likely that the Portuguese would annex and colonised these islands we would end up with the Mascrene Islands, while being fundamentally culturally and linguistically Malagasy. Although the Portuguese language and culture would have a major effect. It would be a interesting blend of Portuguese and Malagasy.