As with most cultures and religions, there is some intermingling of customs and credos that develop over time. This is called cultural assimilation in sociology. For example, when the Romans brought Christianity to Celtic-held regions, the Celts accepted some aspects of Christianity and held on to some aspects of polytheism. This fusion is referred to as Celtic Christianity: symbols, folkways, and rituals of Christianity are tinged with the symbols, folkways, and rituals of Celtic tribal religion. One example is the embodiment of St. Brigid as the patron saint of Ireland; Brigid was an early Iron Age goddess of fertility in Celtic Ireland. The pagan holiday Imbolc celebrated Brigid as the goddess of spring, crops, and fertility; Imbolc was selected as St. Brigid's feast day by the Catholic church.
Another example of this cultural assimilation would be the outgrowth of Christianity from Judaism, and the outgrowth of Protestantism from Catholicism. There are many examples of shared beliefs and rituals between Judaism and Christianity, though their central dogmas are different. The same goes for Protestantism; when branches of protestants began breaking away from the Catholic church, some of the new religions were virtually identical to Catholicism, like the Anglican/Episcopal church. Others went further afield from Catholic ritual but kept many of the central beliefs of the Catholic church, like the Quakers.
So, to sum up, the influence of Hinduism as a cultural foundation for Indian Muslims would provide for a belief that seems similar to the caste system. Incorporating the caste system into Islam would make it easier to convert Indians to Islam, because the structure is not a major leap from what they are familiar with. This structure would also make it easier, theoretically, for Muslims and Hindus to live alongside one another in a social order everyone has in common.