I just got mine in January. I hadn't changed my birth certificate so I included the legal name change order from the court. Part of the supporting documents for the name change was a letter from my doctor certifying the change of gender. I, too, opted for expedited service and both card and book came back showing Female.
Once they returned my original documents, I sent them to Pennsylvania to correct my birth certificate. That is still pending. They cashed my check, so I assume the application was not rejected. If the certificate comes back with an indication that it was changed, corrected, or amended in any way, I will never use it. I will use the passport instead. If it does not indicate any change, it will support what my passport shows, so I think it will be ok.