Is it permissible to eat from the father's surplus money that he adds to the funds allocated for expenses, with which he buys food, knowing that the father used to pay the deficit from his own pocket?

The argument your father made for taking money from the embellishments of Satan is that the money belongs to the students, not the university. He should use it as mentioned in Fatwa no. 159118.

Even if the money belonged to the university, your father is not permitted to take it preemptively due to perceived injustice. Rather, he should demand the removal of injustice through lawful means.

It is permissible for you to eat from your father's food because his money is mixed and lawful, unless you know that a specific food item was purchased with unlawfully obtained money, in which case it is forbidden for you to eat it except out of necessity.