Consent is an on-going thing. You don't say yes and are then obligated to have sex. Either (or any) partner is allowed to change their mind at any time during the proceeding. Your spouse can rape you just as much as a stranger - we have progressed from the days where the wedding ring was consent you could not rescind if you were a woman, for example.
In addition, you are allowed to consent to some things and not to others. You can say 'yes, but only with a condom' or 'yes, but only this sex act, not another.' This is why Assange is accused of rape, as he had sex without condom with someone whose consent was only given if he used a condom. If you consent to vaginal sex, and then your partner anally penetrates you without your consent, that is rape, even though you consented to sex.
Furthermore, this app continues the idiotic anf frankly damaging idea that you can rape someone 'by accident.' Rapists don't care about their victim's consent. This trope that men are bumbling fools who are to stupid to ascertain whether a woman really wants to have sex, and on the other side of the coin, that women cannot rape men because men always want sex, is utter bullshit. (Not to mention homophobic, and 'misandric')
And finally, a rapist has no concern for their victim's boundaries - do you really think they will have any compunction about forcing their victim into 'consenting' in the app? Or simply forging the consent?
These app makers have misunderstood what consent is, and therefore what rape is. Consent is an ongoing process, not a single data point.