Most Muslims in India and Pakistan can trace their roots back to Muslim invaders
There have been lot of migration from Islamic countries in West to Bharat. But majority of Muslims in Bharat and Pakistan are original inhabitants of land who converted to Islam.
Secondly, even the outsiders were mixed with original inhabitants. For example, Mughals were originally Turkish speaking Mongoloid people, but after several inter marriages with original inhabitants, their countenance changed and they started speaking Urdu.