I empathize, I've had moments where I was confused about someone's gender as well. I understand that you want to explicitly express your confusion, but I personally don't think it's all that helpful and, as you said yourself, it only spreads further confusion. If you are confused as to someone's gender, then I believe that the most straightforward way is to simply ask how they want to be addressed.
The confusion has already been expressed by someone deliberately defying the social norms indicating gender, mating status, character, and so on based on their own internal gender conflict/confusion. Which then confuses and conflicts everyone else. Some people will quickly be able to embrace this new variant in social status, but many will take longer, and some will find it very difficult to ever accept or adapt.
This is not society's fault. Nor is it necessarily society's obligation to accept this new variant in it's social norms, at all.
That's the point I'm trying to make.
"Liberals" (of which I am notoriously one) have an annoying tendency to just assume, blindly, that the changes they want to see happen in society are for the better, and that it is therefor society's obligation to adopt and implement those changes. LIBERALS ARE OFTEN GUILTY of the blind arrogance that conservatives so often accuse them of. And I think this is just one example of this, among many.
As for why refusing to recognize other sis denying their humanity:
Gender identity is integral to everyone's identity as a person. Just as your identity as a male is an integral part of your identity as a human person. You are refusing to recognize this person as the gender they identify as, and therefore refuse to recognize a part of their identity as a person.
Our internalized gender identification is not at issue, here. It's how we choose to 'signal' ourselves in that regard, to others, that is at issue. And also the fact that our society does not currently have a comfortable set of categories, labels, and signals to designate one as being within one of these anomalous categories of relatively rare gender conflicted/confused folks. The necessary mechanisms of social specificity just don't exist, yet, and until they do people will get confused and probably resentful toward those causing that confusion, when they find themselves being confronted by it.
Which brings me back to my question, which you haven't answered:
What is the "cost" of recognizing other people's gender identities?
The cost is the disruption of social cohesion, peace, order, and comfort.
What sacrifice do you have to make when you recognize somebody's gender identity as valid?
I had to change my concept of gender identity, and my perception of 'reality' as I knew it. And this is no small thing to ask of anyone.
And what price does everyone else have to pay in order to recognize your gender identity, and why don't we get to choose?
My gender identity is immediately recognizable, so no one is having to pay any particular cost for it. And you do get to choose how you will present yourself to your fellow citizens, regardless of your internal gender conflict or confusion. The world is what it is. And you are what you are. But you do get to choose how you relate the latter to the former.
You tell them to find a "safer environment" elsewhere even as you are denying them that exact safety.
How can you justify that?
I am not denying anyone anything. I am simply pointing out that you are ONE among MANY. And to forget that, or to presume too much of it, would not be wise.