"Sex" is defined as biological sex, yes.
If an organization wishes to invoke a statutory single-sex exception, they must base it on biology.
The single-sex exceptions in the Equality Act exist to provide a legal shield for organizations that want the right to exclude the opposite sex.
But organisations like WIA are not trying to invoke a legal exception to exclude trans women.
They are voluntarily choosing to include them.
Whether the UK legal system technically categorizes them as a "mixed-sex" organization, they are still a female-led organization exercising their freedom to associate and define their own community standards.
The Supreme Court ruling is about a statutory exception designed for exclusion, not about forcing private, independent groups to stop being inclusive.
"allows for an association to restrict membership".
It allows them to restrict it. It does not mandate it.
If WIA wants to operate as a legally "mixed-sex" organization that focuses on women and trans women in animation, the UK government will not (and is currently not trying to) arrest their official UK-based Community Collective.