Mental. Gym. Nastics.
It's cool because despite appearing to be in middle school this whole time, they suddenly ret-conned it so she isn't- that makes everything fine, right? No. It doesn't.
Even so, fine let's brush that off, and talk about how dating someone way outside of your age bracket is creepy. It's taking advantage of their naivety, what they know about the world and life (likely very little), and ignoring the fact that when HE was likely in high school she was only like 5-6 years old. Heck, let's say she IS 16. He has to be at least, what, 25, 26 probably? 24 if you want to be really generous, maybe 30's if you're not (and she might not have even been alive then while he was in first year). We'll just settle with 10 year gap when he was still in high school. Would you date someone who's a five year old while you're 15? I sure hope not.
At best this story was him grooming her till she reaches an acceptable age for their relationship, at worst it's just plain pedophilia. Either way, it's creepy and I don't know why you'd try to defend it!
Then you put him in a position of direct authority over her life... take her obsessive possessive personality and callousness, get that mess added on top of everything... it's all just so... ugh. I'm sorry if you liked it and was able to look past all that, but I find it kind of upsetting and reprehensible from several objective standpoints.