Both are rare cases. Transgender is more common than intersex as intersex is more complicated since it has series of variations in classification. Why some people are transgender is because their brains do not take in the male or female cells it produces so as a result they end up with feminized brains and masculinized bodies or masculinized brains and feminized bodies. It can cause severe dsyphoria to people dealing with this issue so in attempt to treat themselves in order to live a happy and normal life comfortable in their skin, many undergo lot of hormonal treatment or surgical treatments to make their brain match with their bodies.
In intersex cases, it has lot of classifications, people who are born naturally with a body that doesn't fit into the male or female norms be it in their genitals, hormones, gonads, phenotype, chromosome etc. Some intersex people are also raised up wrongly and undergo dsyphoria too.
Its not easy at all to be transgender or intersex. No its not witchcraft!! Though their cases are different, many of their experiences are similar. To undergo men and women struggle at the same time is a living hell.