It's basically like this.  Military service is conducted by 1% or so the talking heads say.  If we go w/ the 6000 figure of transgenders, out of 1.5 million then even still, it is a small percentage of an even smaller percentage of people affected.  APA still considers "transgenderism" as a psychological disorder.  If you were born w/ boy parts, but deny that you are a boy, and are willing to have a surgery to remove your boy parts, then fine....they can pay for it themselves.  It still doesn't make them a girl, w/ girl parts and having girl things happen to them like menstruation, ovulation, etc.  
About military service?  I personally do not want a soldier who could possibly be suffering from some kind of psychosis to be disrupting good order and discipline because of their personal belief.  The mission comes first, then the team, then the individual.  In that order.  Use all the examples of other country's military all y'all want, but the US military is different from any other.