I’ve read that the transition itself is usually a smaller part in addition to what has been already dealt by nature
This is unfortunately not the case for most trans people. I think it's quite rare that a trans person would consistently be able to pass (=blend in) before HRT.
There are some trans people who are also intersex, which is the condition when one's biological sex (without medical intervention) doesn't fit neatly in either the male or female boxes. But most trans people aren't intersex and about half of intersex people aren't trans.
Edit: But I do agree with your main point, there's simply no way an app like this could identify trans people with the vast range of facial features humans have. It will both exclude many cis women and allow many trans women, as Giggle did a few years ago.