Being a desperate survivor in a wasteland would make sense if the game actually punished either character in the story. As it is, no matter how close the player gets to dying, the cutscenes all play out the same. The story doesn't change to the player's ability as a survivor, it just exists completely separately (Cutscene Joel was always better off than player character Joel during my first playthrough). That's a separation of game and narrative. Being a better player offered no story reward that a worse player didn't receive.

Having optional conversations and dialogue outside of cutscenes doesn't mean it's a part of gameplay either. A button prompt to find out Sarah was a teenage pregnancy still keeps the player a passive entity in the conversation, unable to investigate or press the issue or do anything at all. Again, Joel and Ellie's relationship is the meat of the game, but the player can do very little with it except look at it, and only when the game deems it an appropriate moment to do so. This also applies to Ellie's increasing battle prowess as the campaign progresses; I have no control over what she's going to do and when, which makes her unreliable, and again keeps the relationship in combat between the two main characters completely under the computer's and RNGesus' control.

Your point about environmental story telling is very cool, and something I had forgotten. The sewer level was very well done, and something I wish the game had done more of. The entire game presented a fantastic and varied setting, and each location could have had a different story to tell. This could have also tied back to Joel and Ellie's relationship by having either one react to the new, completely optional story and the other respond in kind, thus placing relationship development in the hands of the player (this is different from a button prompt because instead of just being "Press Triangle", finding this optional content adds a gameplay challenge to accessing it, and rewards better players with more story).

What I've said about being passive in the characters' relationship also applies to your comments about the Giraffe scene and Joel's character; you're nothing more than a silent observer, and you have no agency over the outcome. Placing it outside a cutscene does not make it gameplay.

As for the Hospital level, killing the doctors would have been selfish, coldhearted enough for the character, but churning through countless grunts with a machine gun, expending hundreds of rounds in what was supposed to be an environment where every shot counted, was a complete disregard of the desperation that came before. Again, it was climactic, it was in character, but poor design. As for what the Fireflies could or could not have done, it doesn't matter. It doesn't really pertain to marrying story with gameplay.

In my opinion, being a passive observer outside of a cutscene does not make the story and gameplay any closer. It only reinforces how little agency the player has over the reason the player plays the game.