The Westminster Confession is "The principal subordinate standard of the Church of Scotland" but "with due regard to liberty of opinion in points which do not enter into the substance of the Faith" (V). This formulation represents many years of struggle over the extent to which the confession reflects the Word of God and the struggle of conscience of those who came to believe it did not fully do so (e.g. William Robertson Smith). Some Presbyterian Churches, such as the Free Church of Scotland, have no such "conscience clause".
To the church of Scotland, what is the sub standard doctrine?
The Westminster Confession