Alpha is, quite literally, the alpha dog of the pack. He's a senior who seems to think that he's totally large and in charge at Alabaster, even though he wasn't there the entire year before. As Frankie comes to realize, a lot of what Alpha does is a power play. Like when he pretends not to remember her from the boardwalk, while simultaneously dropping hints that he totally does:
There it was again. The custard. Alpha wanted Frankie to know he remembered. And that, somehow, he was disappointed in her. (14.86)
Alpha hints at the frozen custard incident in order to send Frankie a message that he thinks she's just a girl—one who can't even finish her ice cream by herself. And then there's the fact that he steals Matthew away from her at inopportune times. Total power play. What's more, he pretends that he is the person behind all those prank emails, because he wants to seem like the one calling all the shots, even if he's not.
But that doesn't mean that Alpha is above acknowledging another top dog when he sees one. When everything goes down and Frankie is charged as the culprit behind all the pranks, he sends her a final email letting her know that he admires her:
I'm just writing to say I underestimated you.
I significantly underestimated you. (45.28)
He doesn't have to like her—and he even says so. But he definitely thought that Frankie was just a cute little girl, and that whoever was challenging his position was probably another member of the pack, as in one of the boys that he considered his equal. He never thought that it'd be someone like Frankie, who's just a pretty face to Matthew and his bros.
So while Frankie may not have succeeded in shaking up Matthew's world all that much, it's clear she got through to Alpha, at the very least.