As far as this piece and my own views go, I think its useful to think of violence between Muslims and Hindus as similar to the violence seen earlier between Hindus and Buddhists. Motivated primarily by political and economic incentives. Religious hostility was always a factor, but a tertiary one, and only occasionally bubbling up to the surface to act as the primary instigator for violence.
I think this formulation is true regardless of how differently Hinduism as an ideology and civilization interacted with Islam compared with Buddhism. I also believe its easy to get sucked in to ethereal thoughts about one civilization “traumatizing” another with its stark ideological difference, while in reality the on-the-ground political situation wasn’t that different from before the former arrived.