I agree with you that the numbers are small. You’re right.
One of the concerns is that military-paid gender reassignment treatment and surgery may be an incentive to join the army. The standard first enlistment period is four years. Let’s assume that the pre- and post-op treatment period is 2–3 years (based on what I’ve read via Google searches). A recruit could join, spend much of the first enlistment receiving the medical treatment, then not renew. That’s great for the recruit, but not for the military.
There would be a financial incentive to join the military for the single period (during which the military wouldn’t receive much value because so much of the time would be spent in treatment). Based on what I read in the link below, surgery is quite expensive.
Therefore, the numbers may change depending on the financial incentives.
Based on the link below, transexuals were banned from service prior to 1 July 2016.
I would therefore assume that numbers would increase since eligibility has only recently been established.
