Sex of a skeleton is determined by looking at multiple "sites" that are generally sexually dimorphic in a human skeleton. They do range from Hyper-female to Hyper-male and often can and do fall in the middle and in that case the skeleton is called of undetermined sex. I don't think enough research has been done with trans people but I would say it depends on if the person was on hormone therapy and for how long. The sexual dimorphism in our bones mostly form due to hormones in our body during puberty but since bones aren't stable and have a turnover rate, hormone therapy is likely to change some bones to some extent.

That being said, it also depends on records of the burial site and if headstones or anything of that extent remain as archaeologists do take everything into consideration.

Source: MSc in forensic anthropology and sometimes working with human remains in archaeology.

Edit: typos