Would disagreeing with one's parent regarding fasting two voluntary days and only fasting one day based on their wish be considered an act of disobedience to them?

If the situation is as you described, then you are not being disobedient to your father by differing with him regarding his forbidding you from fasting on Mondays and Thursdays. This is because your fasting is an act of obedience to Allah, and there is no obedience to a creature in disobedience to the Creator. It appears that he intends to show you leniency, not to oblige you to abandon fasting.