The article addresses that. Given all the testing already, this is a trivial addition:

“Under the new policy eligibility will be determined by a one-time gene test, according to the I.O.C. The test, which is already being used in track and field, requires screening via saliva, a cheek swab or a blood sample.“

You think Olympic athletes have any expectation of privacy around drug testing already? They have to register their every move and piss while being visible on demand.

Well the article says a cheek swab or blood test.

You think the only way to medically test for male vs female is to visually id genitals?

The article already covered it: It's minimally invasive (cheek swab) testing typically for the SRY gene - https://en.wikipedia.org/wiki/Sex-determining_region_Y_prote...

This is less invasive than all of the other doping tests that athletes already go through, which require blood draws.