There are women, assigned female at birth, who identify as women, yet are genetically male. For example, women with CAIS:
Socially, we sex on phenotype - so yes, they're usually recorded as female as they have a female phenotype.
It is hurtful to call them men, yes, because they have a female phenotype.
Research in this area has shown a stronger identity connection with phenotype than sex chromosomes as they're not any more likely to have gender dysphoria than anyone else. That's nothing to do with the trans/cis binary & most get that genetically male means male phenotype. Our sex phenotype comes from genetics too, so claiming just sex chromosomes are genetic isn't entirely accurate.
Cis is just a descriptor for someone who is not trans.
No, it means "on the same side."
Dysphoric people who do not identify as trans being categorized as "cis" makes no fucking sense -- you are saying we're on the same side as what distresses us - and erases there are many other ways of viewing gender and gender dysphoria. The trans/cis binary is not universal, many groups around the world have asked for it not to be applied to them as they have a different view of gender diversity. Some are moving away from trans/cis binary and using gender diverse instead in order to actually be inclusive on this topic.
So no, cisgender doesn't mean "not transgender" it means someone who has a very particular view of gender who views themselves within that framework of having a gender on the same side as their sex.
only a minority of variations in sex development are associated with an underlying medical issue which needs treatment. The majority are simply differences in development.
Only a minority are fatal without treatment, the majority - for quality of life reasons - most are recommended to have usually some form of treatments, usually hormonal, as the "differences" are linked to endocrine issues which can have a knock on effect across the body as hormones control bloody everything. In fact, health care access is a big thing for many activists in this area. Erasing the health issues helps no one.
They identify as women and if they want to call themselves women and use her/she etc then that's mighty fine by me.
And that's fine socially.
Legally, there is a different matter. We don't allow people to claim the rights and protections of being British who aren't born British without background checks, references, tests, and such no matter how someone has lived or identifies. I don't think sex should have less consideration than nationality.
Would you rather them use male and get stared at and treated unkindly because that's what happens.
Do you think they don't experience stares or unkindness in single sex women's spaces? Do you think we're all sweetness and light?
Shockingly, no one seemed to mind my being stared at and being treated unkindly in the girls' locker room, but I most certainly was not allowed in the boys' without supervision, even when they allowed me to wrestle with the boys. Some risks were considered too far and we all deserved privacy even if we then wore skin tight unitards.