The article quotes Prof Merbs saying "The skeleton is about as female as can be." but doesn't seem to say in what respect it was female, which is a weird omission.
The family seemingly avoided infant baptism, in which traditionally a child might be stripped naked, so the likelihood of external genital abnormality seems relatively high.
Lots of chromosomal changes result in amennorhea in females. I'm just surprised there is no speculation as to the exact nature of the persons phenotype, particularly their chromosomal makeup.
Female pseudohermaphrodism might explain having testes but being biologically female; similarly true hermaphrodism (eg due to mosaicism, having 46,XX and 46,XY karyotypes).
But perhaps they were male with partial androgen insensitivity syndrom (PAIS, https://en.wikipedia.org/wiki/Partial_androgen_insensitivity...), I'm not sure how that presents itself skeletally and Wikipedia doesn't appear to have any info on how chromosomal abnormalities effect skeletal development. It doesn't seem too wild to imagine a male with PAIS might have a "female skeleton" as skeleton differentiation develops through puberty, at least one doc I read [oup.com link] indicated - but not explicitly - that AIS would lead to a female skeleton.
Some sources:
* https://academic.oup.com/edrv/article/39/5/803/5052770
* https://www.researchgate.net/figure/Partial-androgen-insensi...
Though uncommon, XX children can have ambiguous genitalia at birth. Today (1) we have some idea on what it is and we can deal with it at various stages of growth in-utero, at birth, during infant development, at adolescence or even later? Faced with a similar situation the past, parents gambled (aided with biases and superstitions). Is that sufficient to call it idiocy, I do not think so.
1. https://childrensnational.org/choose-childrens/conditions-an...
I wouldn't be surprised to hear of parents who really wanted a boy, birthed a girl instead, and decided to raise her as a boy.
When a boy was born, the boy was dressed up in "girl's" clothes and treated in every way as a girl.
The woman was mad but not mad enough to have her kid taken away from her.