I think they are quite different issues.
After integration, the goal was to treat all participants in the armed forces the same, regardless of race. Whether you were black or white or whatever race, you slept in the same barracks, served in the same conditions, were eligible for the same educational programs, etc. From a practical point of view, members of different races were assigned to different locations around the world without distinction by race.
In contrast, transexuals could require quite different treatment. For example, if the armed forces are required to provide and pay for the hormone treatment and surgery to change a person’s physical sexual characteristics, I understand that the process requires multiple years of preparation and recovery. Since the army offers a two- to four-year enlistment period, then a transexual can spend much of that period unavailable for standard assignment.
In short, a pre-op transexual who joins the military may be unavailable for assignment to isolated environments for a significant percentage of their enlistment. This is a completely different issue than racial integration.
