The issue, as explained to me a year ago by an army medical officer, was that while people are transitioning they are not eligible to deploy. As transitions were determined to take about two years, soldiers who transitioned while active would be ineligible to deploy for almost half of the typical obligation of four years. The debate, as framed to me, was about whether you hire people for a job for four years when they won’t be able to do that job for two of those years.
That said the Trump move is bullshit. Reeks of Pence.