It dues sound as though there is a lot going on here.
You’re a single parent and NC with your father. Her immediate family is significantly reduced. No one’s fault, but it feels she doesn’t have much automatic back up. You’re it, really, aren’t you? so she’s going to be more over invested in you.
You described her as like Sheldon. Isn’t Sheldon autistic? It does sound like she’s struggling with family roles and social norms, which is quite classically autistic. And in girls we often see that they mask very effectively until social relationships get more complex in teen years and they can’t mask, or masking becomes so effortful that it tears them up.
It’s not acceptable behaviour, and you should definitely retain your privacy and not change your behaviour to accommodate hers. Punish her if you like, but try to understand that she’s showing you boundaries are hard for her and wonder why. I suspect you will not see much change unless you address the root cause.
Also remember that at 15 your relationship is transitioning into adult relationship. She will expect, sometimes fairly and sometimes not, to be treated like an adult. You can’t always choose that - especially when she’s behaving like a child. But very soon you won’t have power any more. Only influence. And if you rely on power and punishment to change behaviour, it’s hard to develop genuine influence. Especially if you are asking for something you aren’t giving. That’s why the smoking is so hard. It is something an adult who loves you would also be concerned about, and yes you can do it if you want. But, very soon, so can she. And she knows that. She was probably shocked and scared.
I’ll never forget seeing my mother drink alone for the first time. We we brought up around social drinking, in itself it was no big deal. But when I saw her drink alone, at home, on a school night for the first time I was HORRIFIED! I mean, she’d probably been doing it for years when I was in bed, and my dad worked some nights and really it was nothing. But I was SO worried. She might die. She’d need a liver transplant. She was an alcoholic, we’d lose our home, she’d lose her job, she was an actual person who didn’t obey all the rules and sometimes did stuff she told me I shouldn’t! OMG!
Of course it was fine. I was a dramatic teen discovering my mother was not perfect. It made me anxious and scared. I don’t know where picked up the idea about drinking alone, but I imagine any teen could easily feel like that about cigarettes. And of course if she has a couple, you won’t have a moral leg to stand on, now. You can’t say it’s ok for adults. If you really thought it was you wouldn’t be hiding it.
The line between privacy (which is normal and expected) and secrecy (which implies illicit behaviour) is very fine and quite variable by person. It’s a hard line to walk. I don’t envy you finding it. You are ABSOLUTELY entitled to privacy and to curb her behaviour, although I expect a consequences route will create further issues. But secrecy is unhelpful for children and often makes them more anxious. It often involves nuance that is beyond them. It’s tempting to view this as controlling behaviour, and in an adult it would be. But she isn’t quite an adult. It’s tough. I hope you can find more heave fur both if you, and I think some outside help would be useful guidance if you can access it.