Yes the policy “allows” for that, but the decision solely lies with FIDE. And the examples they give are of deranking. What they mean by that is not Changing Womens Grandmaster into a general Grandmaster. The requirements for a GM are higher. You need 2500 ELO and perform three “norms” of 2600 performance rating. Essentially have high ELO and show against other GMs your skill. For a WGM you need an ELO of 2300 and three “norms” of 2400 performance rating.
Since a WGM doesn’t meet the GM requirements (otherwise they would be a GM) they can’t get that title. But now they’re stripped of their WGM title as well and placed in rank of FIDE master, which requires “only” an ELO of 2300, and no norms. As such it is lower than WGM.
A player at that level is already well connected and known in the community. They wouldn’t be able to keep their transition secret, what with the rumour mill going around. Plus the decision of whether they want to “derank”, giving up their earned title for a lower but more gender-affirming one, should ultimately lie with the person and not with the body that already bestowed that title on them.