i think it has absolutely nothing to do with who that person is you choose over in the 3rd scene is, so it isn't important that it is Emma. it could be anyone for that matter. you have to see this more in a progression kind of way.
1st scene you may choose Cherry and Alison just thinks that the chance with Ian slipped by, so she rather out of desperation to validate that she is still alluring, falls onto Jeremy as backup. kind of like a self-pity fuck.
2nd scene Ian actually chooses to go after her, despite Alison having gone to Jeremy before, but also she has no competition in that scene. Ian and Alison are alone there, so Ian choosing her is (for her) the only logical option Ian could take.
3rd scene Ian chooses Emma over Alison. keep in mind that now after Ian persued Alison, when there was no competition, now there is another girl there (Emma) and he chooses her instead of Alison. so Ian repeatedly chooses other girls over Alison and that is practically telling her she is Ian's backup plan.
now of course Jeremy is Alison's backup plan, but he is totally ok with that, it doesn't really matter to him as long as he gets some action.
Alison is however not ok being a backup plan, because she has feelings for Ian.
what i think
BloodyMares meant with "alpha bitch" is actually just her self-esteem as being (the most) desirable amidst other girls, which Ian however doesn't reciprocate.
so basically i would say Alison isn't angry about Ian choosing Emma, she is angry that the guy she likes treats her unabashedely as backup plan