No, you made sense. My mom surprised the hell out of me when my little brother began his transition (female to male). Conservative as hell and is not just accepting of it but trying to learn more about it (she was misinformed, much like your mother).
From my perspective, try not to think yourself a burden on your mom. Trust me when I say being a parent is hard, and especially difficult when you can't save your kid's world, but it's not ever a burden. Ever. You want to carry your kid's weight so that they can have a better chance. It's selfless. You want the world for them, and regardless if they let you, you'll work your *** off to make it so. You're not a burden, you're her kid.

"She was honest and said that she feels unhappy and sometimes she thinks she would be better off if she was alone because she doesn't know how to interact with me anymore."

She sounds frustrated. My mom said that same thing once when I was twelve. She left me with my dad a few months after and I watched her out the back window as my dad drove off. I truly believed I made her so sad that she didn't want me. Turns out, she was going to get help and get better so that she could be a better mom to me. I didn't learn this until I was eighteen.
I don't think you have to worry about your mom leaving you but I think that your mom is in a similar place as mine was. Wanting to figure some way out to be able to understand, again, maybe? I don't know, I'm not her but she does sound similar to that certain experience with my own mother.