Just playing Devil's Advocate to keep the convo going and to explore different talking points. It's shown that Ian was extremely shy and maybe even somewhat depressed during hs (Was he also dating Gillian at the time? Idk) so of course he wasn't going to notice Allison, especially since she's being coy. Don't know where you're getting Ian needing to give her permission from. Also, making the first move isn't so brazen like you say. If she really liked Ian and she wanted to know where he stands with her she could've straight up asked him about it before monkey branching to Jeremy. From a game pov, I get having Ian (the player) chase her but I'm not talking about game mechanics, I'm just talking about the character on her own separate from that.
Perhaps Alison was a bit shy in high school to confess her attraction and didn't want to risk her friendship with Ian. I mean, probably all of us had friends in school who we were attracted to but didn't have the courage to confess and potentially screw the friendship, so it's not so hard to imagine her frustration with Ian who doesn't notice her as something more than a friend.
Also, Alison lays HEAVY hints for Ian that she's available and interested. I mean, you have to be blind like Perry not to recognize them. Let's examine her behavior.
1) She calls Ian and asks to have lunch with him. Jeremy picks up on it right away and tells Ian to go. Ian also has an obligation to Holly, so he might have to refuse. If he chooses to go and tells her words of encouragement, it's a done deal between them. After that Alison does everything in her power to seduce Ian: send a selfie, asking if he likes the photo; flirt with Ian in the bar, asking him to come with her when she goes to get the drinks; if Ian picks up on those hints and shows his interest, she dismisses Jeremy's advances and tries to focus Ian's attention on her.
2) If Ian meets her with the others, then she thinks that Ian is the same old doofus and expresses her interest in Jeremy. However, if Ian tells her that he'd like to meet her more often, then she's curious to continue.
3) She asks Ian what he thinks of her (She can't get more obvious than this), gauging Ian's interest.
4) If Ian played his cards right up to this moment, then Alison starts flirting with Ian and then goes for the drinks to see if he'd follow. If he goes to help her with the drinks, she straght-up asks him why he didn't hit on her in high school. I mean, it's a pretty blatant first move in my book. If Ian doesn't beat around the bush and goes for it, then it's sealed.
5) If up to this point Ian was coy and didn't express his interest openly, Alison starts to lose hope on Ian and consider going for Jeremy instead, because he doesn't beat around the bush and shows his appreciation clearly. If Ian paid attention to Alison previously and wants to up his game by flirting with Alison (finally!), then he easily gets her interest back and goes home with her.
After all that, it's a bit unfair accusing her in dishonesty or preferring Jeremy. All of her behavior is in Ian's favor, he just needs to show some appreciation and make his intentions clear to seal the deal.
You also need to keep in mind that she chooses between Ian and Jeremy, her 2 high-school friends that she knows for a long time. She's not bold or desperate enough to hook up with strangers after all (who would totally be all over her). She wants to celebrate her freedom with people she trusts. She tries to act confident but she's not confident enough to straight-up tell "Hey, Ian, now that we're both free... do you find me sexy?" so that's why she uses hints to gauge his interest first.