It is geographically not possible for Indians to have come from Indonesia. You may be right on the others though...makes sense.
IMO, the migration would have been the other way round, from India to South East Asia and Australia (considering the fact that Indonesia is a bunch of islands in the middle of nowhere).
It wasn't that way during the Ice Age. There was a land area there (Sundaland) that was twice the size of present day India. Also, it was nice and warm and humans, of all sorts, must have thrived while the Neanderthals over in Europe were taking a 'beating'.