How are they different?

Both require the batter to have both feet completely in the batter's box at contact. (They can have only one foot on the ground at the time of contact, but whether it's one or two feet on the ground, both have to be in the box - and the lines are considered IN the box.)

Both treat contact with the ball outside of the box as a dead ball, with the batter out and runners having to return to their bases.

There is a difference on the penalty in NCAA, where the defense has the option to take the result of the play or the penalty for illegal contact.

Maybe you can learn me more?