What happens in a year or two when hormones kick in for your son, he has a girlfriend, and they want to have sex...? Because if your daughter is treading the path of allowing him to behave as though he is an adult, already, then what's to stop her from allowing him and his future girlfriends to have sex at her place, without their parents knowing anything about it? And if a pregnancy occurs, is your daughter in a position to pay the child maintenance, until your son is old enough to leave school, get a FT job and do so himself? Because if it happens under her care, because she has assumed herself to have parental responsibility enough for him, to unilaterally make such decisions/choices regarding him - she needs to be the one to deal with the inevitable consequences.
Such as him getting drunk (because I doubt she's only allowing him to drink wine!) and either vomiting in his sleep and choking to death on it, or otherwise suffering injuries - potentially life-changing ones - whilst under the influence of alcohol which she, as an adult, has provided him with and allowed him to drink without parental consent in her home. Is she prepared to either live with the guilt of being responsible for his death, or to become his FT carer...?
These are all questions that you (calmly) need to ask of her. Because, despite her being an adult, in this case, she's not thinking like one. As another poster said, she's thinking/behaving like the "cool older sibling", and is probably revelling in thumbing her nose at your more sensible, adult, parental rationalisations about what is best for your child.
I'd hazard the guess that the only reason you found out about the alcohol drinking, @Nolitoad, is because your daughter forgot that you/their dad don't approve of your 13 year old child drinking (yet). Your daughter's an adult - she can freely consent to her own alcohol consumption... your son cannot.
I have children with a similar age gap. My 26 year old constantly tries to undermine me with my 17 year old son - but I will only call her out on it, if it's a parenting issue. If it's something that most siblings get up to? I leave them to it. However, I also know that kids get up to all sorts of (normal) mischief. Drinking without parents knowing, having sex in weird and inventive places, and sadly, experimenting with drugs (will she introduce him to them, too, in a "safe and structured way"?). This generation aren't the first - and they won't be the last. My son lost his virginity when he was 14, which I only found out about last year. My daughter got hideously drunk at 16 and ended up in hospital having her stomach pumped, with my only finding out that the innocent sleepover she'd been at, was another parent behaving like your daughter and allowing a bunch of teenagers to get hideously drunk... when the hospital called me! (And she ended up with Children's Services involved, and a lot of legal letters to read from all of the parents who were oblivious until my daughter and one other - out of 5 guests - ended up in hospital that night!) With my son, there is a lot of frank and open communication - because I learnt the lesson with his sister, the hard way, at times. I daresay that your daughter is like mine, and only wants to protect her little brother... but she's opening herself up to all sorts of problems/issues down the line. Because she isn't mature enough yet to rationally think about these things going down the line into her brother's future. You are. It's why you're the parent... and she isn't.
There needs to be a boundary placement between you/their dad, and your daughter with regards to your son, I'm afraid. Otherwise how can you trust her with his safety during their sibling sleepovers? 