My better half asked this question because she thought you would like to know. The answer was provided by Barry McCain. In the example, John (Owen) Maguire has a son named James. When James reaches maturity he can choose to honor his father either by using Maguire as a surname, or, he can honor him even more by including both his given name and and his surname. Thus, if he calls himself James Maguire McOwen, he is calling himself James Maguire son of Owen. That really does distinguish him by name from the scads of other Maguires.
It is no accident that more than a few men have two surnames in their names.
How can McOwen be considered the same as McCown? Again, Barry McCain provided the answer. There are two Irish Gaelic names that have been used for John and that are pronounced as Owen. The two names in Gaelic are Eoghain and Eoin. So, if a man is named either MacEoghain or MacEoin he is literally the son of John but the modern surname can be something that has a modified form of Owen such as McOwen, McKeon, McKeown, McCown or McKown among many others. They are all sons of John or Johnson.