If a person has the spirit of truth, the spirit leads them into truth that Jesus is the Son and the Father is the One God. Then when they say that Jesus is the Son of God, they mean Son of the One God, and they mean Son of the Father. This is what they mean by saying Jesus is the Son of God. There can be lots of gods, but there is still this Father who is the One True God. This One True God is Father of Jesus. This is the truth to which the Holy Spirit leads them.
