Down "runs", plural, then yes you're correct. We were down 3-2. We were down by 1 the night before and won because we didn't give up on the game. You're conflating 2 different situations. No manager worth anything should ever give up on a 1 run game going into the late innings.
Point of a protest is for the powers that be to notice the protest. The Astros Front Office are not reading this forum. I say enjoy whatever you can get.