We see later in Scripture, after Jesus' discourse about being Pharisees, that Paul addresses himself as father - for I became your father in Christ Jesus through the gospel. And there are numerous places in scripture where the disciples use phrases like "my children", "my son", "my little children" as though they are their father.
And that's the meaning and intention that not only Catholics but also Eastern Orthodox follow. I guess they could address them as, for example, "John, who became my father in Christ Jesus through the gospel". But that becomes cumbersome after a while. So, it is truncated to Father John, but it still has the same meaning and usage as Paul and the other disciples intended.
You seem to be interested in the Eastern Orthodox, so this reference may be useful to you.
Let the spin continue...