Shadowstalker16: People say the reference is just lame, and most people complain about SJW stuff in the game more. Its still overblown, IMO but a simple reference isn't the sole cause.
lunaticox: I think it would be useful to look at this as a "perfect storm" situation.
One has to take into consideration that this is a beloved franchise with a lot of characters that people still care about to this day, now, not only did the developers make their feelings clear about how they didnt like certain aspects of the original game, but also added changes that suited their particular vision of what is acceptable and whats not.
That alone is going to get you in the bad side of a lot of people, regardless of how you go about it.
Now add on top of this the fact that they had the bright idea to make a "joke" about a controversy that is as flammable as you can get, a controversy so flammable in fact that its guaranteed to start a lot of heated arguments on internet forums two years after its inception.
That was a dumb idea, unless the intent was to cause controversy, wich they certainly got in spades.
Add to that the inclusion of characters and themes that are sure to cause even more controversy when not handled properly,
even among those who advocate in favor of them. You can see it for yourself in the steam discussion page, there are currently two threads about transgender people not being very supportive of SoD.
It reminds me of the controversy surrounding Pillars of Eternity.
Add the complaints concerning the overall quality of the expansion, the multiplayer, the bugs, the writing as a whole, the UI...in a good day, devoid of any of the stuff mentioned above, would have certainly affected the perception of the expansion.
And finally add to that the attitude of the developers towards it all, wich didnt help to defuse the situation, asking people to balance review scores is another dumb move, even if you are "in the right", you dont fight fire with fire.
I'm very interested to see the games media's take on this. Something tells me they won't consider all the factors you listed.