It definitely feels like the author is aware of these things, the problems they have, and have been threading that needle very well. I don't think it's anything profound, but it definitely has used the expectations set by those tropes against the reader in a positive way. Like, it's not that she has a cheat skill given to her by the world. She gained access to whatever programming language the world is made in and was able to design her own skills and menus and stuff. The story manages to remain focused by grounding itself in the character relationships rather than the story of the game or anything. And while she is overpowered in many ways, it's only relative to the baseline of the game, rather than the real conflict against the world, and her personality remains in flux rather than being set in stone.Well, I'll be damned. This story is actually GOOD, despite raising sooo many red flags. And not just that, the setting is very well utilized to make the NPC-s, and whole world feel artificial, but still alive at the same time. I'm at a loss of words.
As for the red flags:
- Video game levels and skills (and other stuff like loot chest) in your Manga/Manhwa usually leads to terrible writing entirely focused on "cheating" the system.
 - "Mixer" manhwa, that mixes several tropes and concepts (game world + reincarnation/time loop + martial arts) usually ends up as a terrible unfocused mess.
 - OP protagonists are just hard to write well in general. Same goes for the stoic ice queen type. Their motivations usually don't line up with their personalities.