biological sex is not binary and not just chromosonal.
We do see this phrase in many forms very often.
Biological sex is very stable and has been, in humans, for so long that you can probably say 'forever'. It doesn't require any philosophical discussion or underpinning. It doesn't require any further definition except that there are bodies formed around the production of large gametes and small gametes, regardless of whether that production has, is able to, or will occur in the future. And there are infinite variations of this but they can reliably be sorted.
Those who have a difference in sex development that cannot be categorised as being either a male or a female difference in sex development are very rare.
Biological sex IS binary, there are NO third gametes, there are NO third sexes. You are right, it is not just chromosomes that dictate sex, although the combinations that are not XX and XY are still quite rare and the majority of trans people do not have these medical conditions. Of course, there may be an intersection and there will be some people with differences in sex development who are trans.
It seems that those who wish to strengthen stereotypes are the ones who seek to destabilise the sex categories so that they can change the definitions of the words they wish to use to describe themselves.
However, we are always interested in reading new studies and papers. So maybe you could link up what has formed the basis of your beliefs so we can understand it better.