That argument applies much more to other organizations listed in the report. But even in the article, Beira's Place is described as

a sexual assault support center founded and funded by billionaire J.K. Rowling that explicitly excludes transgender women from its services and was established after Rowling objected to Edinburgh Rape Crisis Centre’s inclusive policies.

She didn't like the way an organization was run, and made her own. The case can be made that it's anti-rights, but thoughtlessly throwing around labels like Amnesty UK did here against someone with the time, money, and motivation to respond with lawyers was an own goal.