Well, this is clearly wrong – it's obvious, for example, that gender identity could have a significant impact on mental health.
Regardless of that, you seem to agree that:
- Sex assigned at birth is important medical information
- Information about gender affirming treatments is important medical information
So I don't think there's much to worry about there.
The problem is that over the past few decades there has been substantial conflation of sex and gender, with many information systems replacing the former with the latter, rather than augmenting data collection with the latter.
I think it's pretty clear to see how discrimination is the cause of that. Why would you volunteer information that from your point of view is more likely to cause a negative interaction than not?
In many places I'd seriously question the motives for asking about either in general. Do you really need gender info to write better targeted spam mails for your SaaS product?