1.- That would be the risk of the player fom choosing that strategy/tactic then.
2.- That would be considered a stage hazard. Just like Brinstar's Lava, or Pictochat's Spikes/different hazards.
3.- You're true with the first line. However, the point of a counterpick is to "Gain advantage in the match up thanks to the Stage", this is why Diddy Kong chooses Final Destination against Meta Knight, because he has the advantage to have more space to maneuver and combo, which in the end, gives him an advantage. Why would King DeDeDe counterpick Donkey Kong to Green Greens? Because he could get an easy Infinite Grab if he grabs Donkey Kong towards any Wall. Which in the end, the stage is giving King DeDeDe an advantage.
The whole point of a counterpick is to gain an advantage over your opponent. Otherwise, we should all agree on 1 stage and only play on that stage, no? That's why we ban a stage, so we don't get "Hard counterpicked", or strike neutrals, in the case of a neutral stage being bad for our character (Yoshi's Island, Final Destination, Lylat Cruise, etc).