Am I right or am I "behind the times"

I commented on a story today about transgender persons and noted that if they have a XX or XY chromosome, biologically they are a man or a woman or boy or girl.
I am not one to pick a fight with the GLBT community and see no purpose in doing so, but realy, I feel that as a physician and scientist, this nomenclature whereby I must refer to a transgender XX as a man or a Transgender XY as a woman makes little sense to me other than I am going to respect their mental and emotional health.  For that reason I am all for the idea of commenting on their gender as they would like to have it spoken.  

Here is an excerpt from my comments on the huffington post article.  I think I articulated my thoughts well, but I do realize that it may have left an unsettling feeling of wrongdoing in the minds of those in the glbt and other communities.  I aim really to be honest intellectually and hope that either my view and feelings will continue to evolve or else my views which may be correct are to be tolerated and respected. 
Either way, I suppose I bit off more than anyone could chew by simply commenting, but I feel that there is an issue of intelligence that is not being considered.  Thanks.

http://www.huffingtonpost.com/social/JewishPhysician/jenna-talackova-transgender-miss-universe_n_1530703_155729771.html