Thank you for the welcome Joanna, I checked out all those things you listed and they are quite helpful with understanding how the site works.
For those that are interested, I will offer some insights from my own preliminary research.
First, the military will continue to only recognize male and female, be it trans or cis. This makes sense from a logistical stand point as it makes planning much easier for a multitude of missions in regards to basic care of those in the service. As well as reduces the amount of regulations that must be amended. I can only speculate that this may eventually be broadened to identify other genders, but there is no evidence at this time. Genetic complications that effect gender physically will still disqualify certain individuals for service; someone who manifests both types of reproductive organs for example. Military members cannot change their gender marker until their transition is deemed complete by a health care provider and appropriate civil documentation is presented to the appropriate branch Human Resources Command.
Second, several regulations are being amended to either be more gender neutral or in the case of "mental disorders that qualify an individual for involuntary separation from service" the term transgender is being completely omitted.
Trans individuals must maintain the physical standards (body fat %, hair cuts, physical fitness, etc.) required of their gender marker on record until their transition is complete as indicated by a health care professional. In addition, trans individuals must present as their gender marker on record while on duty until their transition is completed as stipulated previously. Once transition is complete, they must meet all standards for their new gender marker.
There will be no special bathrooms for transgendered individuals, they will use what ever bathroom matches their gender marker on record. Funny story time, through a screw up I ended up with a door placard with my name on it. One of my guys took it and put it on my bosses door. He turned around and put it on the small single toilet bathroom near our suite of offices and started calling it my office. I'm not out to my unit yet, but I have my own bathroom already.

If or when treatment is deemed medically necessary by a health care professional, that professional will produce a timeline of treatment. For the Army, the timeline can be "reasonably" adjusted due to mission and readiness requirements before final approval by the Brigade Commander (typically a Colonel) of the transitioning soldier.
Currently, Exceptions to Policy waivers will be handled on a case by case basis at a level well beyond the unit. It's hard for me to place a more basic term to it, but essentially the individuals that will approve Exceptions to Policy for transgendered military are working in the Pentagon or near by. For those who do not know what an Exception to Policy is, it is basically asking to be allowed to be out of regulation with a valid reason without getting in trouble.
My first appointment is next Monday, so we will see how that goes. I have a lot of questions and I am extremely excited to begin working with a professional.