There's an argument to be made that Star Trek approaches humanity as the ideal.
I'm not saying I totally agree with it, but I can see where the argument is coming from. You're right, it not about the body or hardware, but that "humanity" (in the broad strokes of the meaning of the word) is the standard by which "normal" proceeds from. And any aberrations to that form (whether through genetic engineering or cybernetics) diminishes it. For example, in his path to be more human, Data sees the acquisition of human emotions (no matter how erratic they can be) as a step in that path, instead of accepting his own android nature as an extension of what it means to be human.
The Starfleet characters, and the Federation they represent, are paragons of a society that has conquered modern day evils, and all of the cultures and species they encounter are aspects of our society that are taken to extremes. So, in the setting, humanity are the witness/observers of the human condition from an ideal perspective.
It's notable that the Founder threat of infiltration and terrorism becomes less and less a problem in the later seasons of DS9. The Section 31 virus arguably put a stop to that threat.