Does Lena talking with Axel in Chapter 3 (even if it is to tell him to fuck off and stop pestering her), have any effect on the story other than her having the option to choose whether to work with him or not? I want to create a playthrough with that choice, but not if it has no real benefits or consequences.
Refusing to even call Axel gives +1 to Lena's wits and she will automatically refuse to work with him in anything.
Calling Axel but then refusing to meet him gives Lena +1 wits and +1 willpower IF she has <2 willpower points and she will automatically refuse to work with him in anything.
Meeting him in the café but not being too friendly gives Lena the option to refuse to work with him in the chapter 6 shoot, being too friendly will make her automatically agree to work with him in the chapter 6 shoot.
So yeah you can gain an extra wits points and potentially an extra willpower if you've been spending most of it early on, but otherwise, aside from some dialogue changes, it should play out more or less the same in the long run as if you just refuse to have Lena work with Axel.