True, they can't, but they can expect some players, and therefore characters, to disagree in certain situations. If our player is going to be a leader of a psuedo-religious organization, then why allow for a disbelief in the Chantry (or the Elven pantheon, or the Stone, or whatever the Vashoth are)? Or why allow elves, dwarves, and qunari to be Andrastian? Because they'll have different ways of rp-ing a character. Or maybe you'd prefer it if they stuck with a fixed protagonist that only agreed with your mindset, all others be damned?
That's not the counterpoint, though. The counter point isn't to get rid of all choice. The counter point is that this particular line of choices is out of alignment with their stance as developers. They've stated that they aren't interested in allowing you to 'disagree' with real-world groups. So they are not going to allow you to 'disagree' with transgenderism. However, in game groups are fair game, which is why you can disagree with Vivienne on mage rights and be openly racist against elves/humans as the other race.
Look, I'm all for 'more choice'. I'm not for adding more choice if it doesn't fit with the devs stance to game making. Or if it allows players to openly 'disagree' with LGBT individuals. Or it if seems out of line with the lore established setting. The only argument that's held any weight at all so far is the one about a Qunari PC being unable to express the same beliefs as Sten. Which, if that were to happen, would seem to conflict lore. But, given that we don't have a Qunari PC, I don't see the reason in taking a Chicken Little approach to the very possibility of it happening in the future at some point.
What's the point of adding this stuff in, though, if they're only going to use it to reinforce the beliefs that only half the population agree with? If they want to put in that stuff, great! But they should use it as an opportunity to open up a discussion (like the scenario I provided above). It would do them much better, and help the tran community out more, if they would explain things to a character who disagrees, instead of assuming their player-base all have the same social mindset.
Because the devs have a personal and professional stance on these issues. That's their perogative and I'm not seeing any evidence that it's hurting their business outside of some negative message board posts (mostly from people who have given them money already, despite also being disappointed by them in the past).
I also think it's slightly disingenuous to pretend as if any of this is in the trans community's best interest. Being able to 'disagree with Krem about transgenderism' is not likely to cause any new revelations on transgenderism from people who aren't already at least somewhat interested in hearing the counter point, right? Wouldn't the opposite be more likely to cause someone to think twice of their beliefs, anyway?