The dungeon minigames are optional and avoidable contents of this game, and tied to the light bdsm choice that players made earlier in the game. Just turn off light bdsm in Chapter 2 and Chapter 5 if I am not mistaken, then you will never have to deal with the dungeon minigames ever again. Players who just want story can just turn off light bdsm which effectively disable the dungeon minigames.
The minigame itself is designed to offer some kind of interactivity so that this game is actually a game and not just a visual novel. It is made to mimic BDSM play that involves tools or toys, bondage or restrain and safe word ( password ). The interactivity/minigame actually makes the BDSM play interesting. It is simply scenes where the MC can safely torture girls for whatever reason. Pick a tool and torture the girl, it wouldn't make sense if that part is made into VN. What happens inside the dungeon, stays inside the dungeon.
IMO Flynn974 really had cools ideas with the dungeon minigames but he simply not able to make it happen yet, or will it ever be considering the story is still the main focus and there are more to tell. Of course it could have been a separate section in the game like in the extra menu for accessing character sheets etc. but Flynn974 is not yet an expert Ren'Py game developer, but competent yes, so don't expect perfection right away is all I am saying.