Actually, both of those are quite common occurrences.
I think you're comparing grapes and potatoes.
Transgender integration will likely be easier military wide, but more difficult on an individual unit level, for the fact that there are so few of them in military service that most people wouldn't be exposed to one right away, where as with pre-dadt repeal there were gays and lesbians at pretty much every command, so people got exposed to what made them uncomfortable right away. Units with a trans are going to have to deal with the new normal.
The one transgender I personally knew on Active Duty was a Marine in my VT squadron. Getting to know him on a personal level allowed me to ask questions about "how" and "why" so I could understand more about his indenifying as a woman. While I couldn't personally relate to all of what he said, the conversation allowed me to humanize people in similar situations where before my only interactions with transtype individuals were what I considered to be creepy dudes dressed as chicks trying to grab my dick...
That stigma is likely a common one, and is the reason traing is needed. Someone needs to tell Marines that transgender individuals are humans to, and that they're not just for sex on deployment anymore because integrity, and all that. They're certainly not going to change on their own so someone has to lead from the front, regardless of whether or not they agree with the shift in cultural norms.