His wife paid to be registered as non-domiciled in this country. Yes, her father was deemed to be domiciled in India at the time of her birth, and therefore her domicile of origin is India.
However, a non-domiciled person is someone who has their permanent home outside of the UK. Therefore, it would be assumed that by being registered as non-domiciled here, Mrs Sunak is not intending to stay here. As they are a family, that would mean that Mr Sunak would also not be intending to stay here.
I'm sure Mrs Sunak paid what she needed to as a non-dom, and it is clear that her domicile of origin was not the UK, but the issue is more whether she really is intending to move back to India. I am surprised that nobody has asked her/Mr Sunak that directly, in the circumstances.
Having someone as the PM or even Chancellor who does not intend to make this his (and his family's) permanent home suggests that, actually, they would not necessarily act in the country's best interests.