At that point, it really becomes a question of balance rather than realism. Adding too much benefit to a single activity (which already has two, raising both affection and accuracy) will skew the balance, so I will likely not change that. The MC will have to make do with the dirt he gets on him :)
That said, there will be other ways of increasing MCs own attributes.
I see. So 2 is the max? Then how about adding the stat increase to the pc only after Darkness no longer gets more benefit? That would still keep it at two at any one time. Besides, of all the activities, I wouldn't mind actually training to be the one that is a little OP.
You could even justify it in universe, that once Darkness states to hit her targets, training with her now allows to train the PC's dodge or protection stat, as protecting or dodging is only possible, when the attack has a chance to hit, and thus dodged or protected against.
For further balancing, you could add more benefits to the other repeatable actions with the others, like Megumin's explosion walks could train her accuracy too, and it could serve as strength or dodge training for the PC, who walks long distances with a load on his back.
Aqua's repeatable activity is drinking, and it is Aqua's, so it is fine if it stays a useless drain of money besides raising her affection, or if it only raised a joke stat, like alcohol resistance.
Same with the other girls, spending time and doing stuff together with the PC day by day, could, and should help both of them improve themselves in some way. If higher level areas were added to the game later, adjusting them to account for the increase in stats, could prevent getting it too imballaced, too.
But that is just my take on it.
