Might they not take the same position that is used with base coaches, i.e., the coach must remain in the coach's box but it is not enforced unless the other team complains. And if that happens, it will be enforced against both teams.it's probably not been officially discussed by MLB – I'd have no problem with an ump playing it safe and requiring the pitcher to play without it under "uncontested" circumstances.
If one of your team's pitchers was not allowed to use a card while the other team's was, and your team lost, I suspect the game would be appealed, forcing MLB to make a ruling.