In real life you would in addition always set up a safe word or sth
In real life in a relationship where you know what you're doing, yeah.
These are 16 year old girls re-inventing power dynamics on their own, from scratch or from Aya's eromanga consumption -- which, you know, does not always make a big deal out of consent. With the complication of their sort of consensual non-consent of "I'm buying you so I can do what I want".
(I've also read a claim that Japanese BDSM isn't so into safewords, instead favoring a dom's careful attention. Did Aya show that? Maybe not convincingly, but she got away with it: Marika melted in her hands and got more attached. OTOH, Aya does bring up safewords in a later novel. Maybe she'd done more research by then.)
they always have the top at least stop
I'm almost certain "always" is not true, though I don't have examples to mind.
Marika is actively being raped by Aya especially in the beginning of the manga,
I wouldn't say that. The big rapey scene is chapter 8, where Marika says "I don't want sex today" and Aya pushes forward anyway. Beginning of the manga? Marika can just leave, she's not being held down, she's not being economically coerced (she wants money for an expensive purse.) Things go in a weird direction for her, but purse and pride mean it's worth it to her to stay despite reading porn and getting groped.
(Or because of reading porn and getting groped, depending on how you read her evolution.)
Aya and Marika have such power imbalance to the point where Aya talks about buying Marika.
Aya talks about it yeah, she's probably getting off on it. She has no actual compulsive power, especially not to keep Marika coming back.