I get the sentiment, but I could use the same arguments against HRT, which isn’t exactly what you want.
Bodily autonomy is fine, as long as it’s not harming anyone (including oneself). If this tool is accurate (again, big if), it could actually increase bodily autonomy, since you could distinguish between real cases and those who really have other problems. That takes the burden of proof away from trans people.
Think about how long it takes today from the first visit at a doctor’s office until actual treatment or legal processes can start. Using diagnostics like this, this could be shrunken down to one MRI.