It matters in the sense that you don't get to choose: you have to use the one that your program tells you to use.
This. But..... My feeling for this is APA, Chicago, MLA...in that order. But that's just a gut feel. Coincidentally, neither of my programs dictated it. You could use any style. And when you chose a style, you weren't held to it. But both schools required you to be consistent throughout your document, citing the same types of sources the same way. (I used APA both times because it was easier both in style and to produce citations using software. But even my most recent experience is now a decade old, so I can't even offer an authoritative opinion on that anymore.)
I like APA. Rarely I've been forced to use Chicago and really dislike it. Haven't used MLA since high school English. (Incidentally: citation style is field-driven.)
Hello! I am used to Harvard citation rules for my BBA, but I forgot that UCAM in Spain demanded Vancouver for my Teaching Certificate. That caused some points to get lost... :-( Best regards. Mac Juli