Honestly, the lore is pretty irrelevant here and feels like grasping at straws after the dev got backlash for revealing the fugly face. The issue is that the series started with a hot, faceless main character that had mystery and appeal and then got an apocalyptic downgrade by revealing her face that ended up being less appealing than a smooth, featureless surface. It doesn't really matter that there's a "lore reason" for it.
You make a good point, but Haydee's face behind the mask was already revealed in the first game, where her "real face" is shown on ammo boxes and key cards. Since very few players finish any of the three Haydee games, most remain unaware of this.
The lore is actually relevant in the third game, at least more than in the second, and players can change her face back to the original masked version.
The lore I provided is highly condensed and most of the players will never come up with it by themself and don't know what or how this game is the way it is. The game never straightforwardly tells you what happened and why. Players need every hint to piece it together, need to connect all the dots themselves, and then come up with reasonable explanations. The developer only confirms our suspicions once enough players have figured out the correct answers.
In short, the lore was never explicitly presented, like in games like Ace Attorney or shows like Detective Conan. If you already know who the suspect is before watching it story, many of the "details" can feel unnecessary. However, if you don't know what actually happened, the lore fits quite well.
Also, if you don't like the human face, you can always change it back to the robot mask in the game's menu.
But I completely agree if the human face has to be shown the character's design should be more sexy and beautiful than the current one.