The available evidence indicates that Khelif is actually male: two blood tests from two independent labs revealing an XY karyotype, a member of Khelif's training team describing problems with hormones and chromosomes and that Khelif has been on medication to adjust testosterone to within the female range, and a leaked medical report which describes Khelif as having the male-specific disorder of sexual development 5-alpha reductase deficiency (5-ARD).
This implies that Khelif is not female but is male, and went through male puberty, therefore having the male physical advantage in sport caused by male sexual development.
No, just erroneously assumed to be female and issued with identity documents stating this.
Same as has happened previously with other male athletes in women's sports, such as Caster Semenya who also has 5-ARD and also competed in the Olympics, back in 2016 in the women's 800m track event, winning gold. The silver and bronze medals were taken by males too.
Khelif does not identify as trans, and described such accusations as "a big shame for my family, for the honor of my family, for the honor of Algeria, for the women of Algeria and especially the Arab world."
This implies that Khelif is not female but is male, and went through male puberty, therefore having the male physical advantage in sport caused by male sexual development.