There are a couple of things wrong with this question.
“ given that they all have their origins in the Malay/Indonesian language? “
This is false. Tagalog, Bisaya, Ilocano, and many of the local languages, as well as the many local languages of Malaysia and Indonesia, are all part of the Austronesian language family. Which all come from Taiwan.
The Out-of-Taiwan Theory shows how Austronesians spread from Taiwan to the rest of Maritime Southeast Asia.
As for the diversity of languages spoken in the Philippines, it's the same reason why there is a diversity of languages spoken in Malaysia, Indonesia, and even in most neighboring countries like Vietnam, Myanmar, and Thailand. In Maritime Southeast Asia, many different island groups allow for different groups of people, or tribes, to develop their own distinct cultures, and thus their own languages.
- Ethnic Groups of Indonesia
Not to mention the other form of geographic barriers and features such as mountains and valleys or even open seas that create distinct cultural groups. This is true throughout Southeast Asia and throughout many parts of the world. Monocultures are quite rare in general.
- Ifugao people of the mountains in the Cordilleras.
- Maranao, people of the lake in Lake Lanao.
- Sama-Bajau people are known for living on the open seas.
- Panay-Bukidnon, known for living in the Visayan highlands.
