I also use the VA health system for my medical care. I was previously going to a private MD physician for my care, but we had a disagreement over HRT. So I switched to VA care.
About 6 or 7 years ago the VA published a formal policy that applies to all VA hospitals that spelled out what care is freely available at the VA for transgender veterans. The VA will provide counselling, medications, lab tests and voice training. At this time they do not provide any gender conformation surgery or electrolysis. Depending on your geographical location, some VA's have strong transgender programs and other may be just meeting minimum standards.
As you most probably know, in the VA system everything goes through your primary care physician. Ask for counselling to get your HRT letter, then ask for an appointment with an Endocrinologist for the HRT prescriptions. Somewhere in the mix you will be asked to sign a liability release that you are aware of the risks and benefits of HRT. If you desire voice therapy, your primary care can arrange that as well.
I live in the Miami area and our VA is well versed on transgender care. I have nothing but praise for the care I received at the VA hospital.