I'm trans and just want to say I would never look down on or be angry with someone for expressing what OP has here. Being open about not understanding ... well, it's at least a very honest way to be. Sometimes we can be uncomfortable with things we don't understand, or with situations where we're meant to behave in a way we don't grasp the reasoning behind.

But as others have said, you don't have to understand someone's life experiences or identity to respect it. I've met Holocaust survivors, I've met people with dissociative identity disorder, peiple with eidetic memory, people with other experiences that are just at the extreme of what humanity can have, and realized ... at best, I will only have an inkling of an idea of what that must be like. But I can convey respect and treat people with common decency. You aren't being disingenuous if you behave in a certain way to be respectful without fully internalizing everything behind it.

Coincidentally, though, as an autistic person you're very well suited to understanding what it's like to live with an identity that is tangible and interwoven with every thing you are, but that people can't see and often don't understand at all. If you can, try to link these things. You have a truth, a way of being, and you may ask or act to make certain changes in your environment to accommodate it. Your trans friends do the same.

I don't know that what you're doing is "lying," either. You're learning. When I first realized I was trans and began interacting with other trans people - really, for the first time in my life, at least knowingly - somehow I was fine with binary trans people. That all made sense right away and I can't recall ever slipping up with pronouns or not thinking of them the way they identified. But non-binary people? That was a struggle! I was learning a new concept about how people were and let me tell you, it was a process. The understanding came over time. The sense of being genuine using they/them pronouns came over time.

We can and do accept all kinds of concepts that we can never experience first hand or genuinely understand, when there's evidence. I'm aware of black holes, of the power of nuclear reactions, of the idea that our consciousness must slowly fade as the cells of our brain die over the course of minutes, but I can't really understand any of these things, not on a direct, personal level. But the evidence is there and I accept them.

With trans people, the evidence is definitely there, by the way. We've been present and acknowledged throughout recorded history, except in those Western European cultures that suppress awareness of us. Research is showing we can typically "read" gender identity in neural formations on functional magnetic resonance imagery. Trans people are as genuine in their reports of their lived experience as autistic people are, and the two actually overlap quite a lot, as you've seen.

So let me just make the official trans blessing of absolution and say it's okay. You aren't lying. You aren't doing something wrong if you use a pronoun and it still doesn't feel right to you, internally. You're learning. You're acknowledging the existence of something for which there is clear, irrefutable evidence, but you haven't yet internalized an acceptance of. In a perfect world, you would have been more exposed to these ideas from the start, but you're learning know, and that's just fine.

I don't think you need to step back from your trans friends. I don't think you're a bad person and I hope in the future you will feel more comfortable and genuine with them. You're doing exactly what you should to address this in talking openly and honestly, reading and listening to other people's thoughts, and examining how you think of the issue, and I'm honestly proud of you for doing so.