Well.., Indonesian made up of hundreds of ethnic groups to begin with. Although most are Austronesian stock, some slight differences in skin tone, bone structure and looks are noticeable amongs them. The majorities here are Javanese, Sundanese, Malay, Madurese, Batak and Minang.
In Majapahit case, it is common for kings to have non-Javanese (foreign) spouse, as queen or concubine. Majapahit kings are known to married Sumatran Malay, Cham, and Chinese princesses. It is likely that they have Indian wife too.
Typical Javanese look can be found in this actors playing Arya Kamandanu in Tutur Tinular TV drama about Majapahit era.
The newer 2011 version is pop one with looks somewhat more East Asian, Korean and Chinese historical TV drama influence?