Yes, I have served on protest committees before as the Umpiring coordinator for several tourneys...
I believe you already know the answer to this...there is usually no advantage to filing or reviewing or upholding a protest on a rule misapplication if the call in question does not adversely affect the protesting team's chances of winning the game.....
But the committee will decide if you do move on to protest....so here is the OBR rule on protesting games...
4.19 PROTESTING GAMES. Each league shall adopt rules governing procedure for protesting a game, when a manager claims that an umpire's decision is in violation of these rules.
No protest shall ever be permitted on judgment decisions by the umpire. In all protested games, the decision of the League President shall be final.
Even if it is held that the protested decision violated the rules, no replay of the game will be ordered unless in the opinion of the League President the violation adversely affected the protesting team's chances of winning the game.