What is the ruling on working in the design and printing of book covers for Christians and all their religious publications, as well as designing tobacco (mu‘assal) boxes? And how should one deal with a father's refusal in the event of impermissibility? And should one stop immediately or gradually?

For a Muslim to be permitted to work for a non-Muslim, the work must not involve anything forbidden, nor anything that glorifies their religion, such as packaging their religious books or designing cigarette factory boxes. All of that constitutes cooperation in sin and transgression. The fact that the work is in your father's printing press does not justify the action, for obedience to a father is in what is right, not in disobedience. As for how to refuse the command, it should be done with wisdom, reminding the father of the Islamic ruling and the obligation to obey Allah. If he does not respond, then it is obligatory to utterly refuse forbidden matters, and this is not considered disobedience to parents.