Hi keralaguy. Most Hindus in Indonesia are native Indonesians. But you would find it different with Indian Hinduism, as we love to syncretize. You would see strong influence of our native Austronesian religions and also a bit of Buddhism in our form of Hinduism. The only ones who practice the same form of Hinduism as in India are Indian Indonesians, and there aren't many of them, not like in Malaysia or Singapore.
About Malaysia, I don't think they are intolerant, if they are why are there a lot of Malaysian people of Indian descents? There's gotta be a reason why they decide to take upon their new homeland. When I see Indian Malaysians and Malay Malaysian, I think most of the times they live in harmony. You can see that the popular spot for eating for the Malays are the Mamak Stalls, usually owned by an Indian.