Funny, they don’t force me to take a different from the usual stance. Also, they are an alternative for the full squat in the fall and winter, not an assistance exercise. In the season, together with Olympic lifts, box squats are the staple of my lifting, just higher than in the previous months.
What type of stance do you usually use? Most people who do box squats do them the Westside way and that’s where the problems can come from. The Westside way involves a mostly upright torso and a very wide stance. This can cause activation issues, but not for everyone (like you, apparently).
I still wouldn’t recommend them, though particularly talented and/or coordinated athletes can do fine with them (or with anything else, for that matter).