Ephesians 4:5 in context is a reference to the unity of believers in the Spirit. Christ has brought down the barrier that divided Jew from Gentile. Both believing Jews and believing Gentiles have one Lord, one faith, etc.

His reference to baptism may be related to his earlier reference in the same letter to circumcision (2:11-22) which was an outward sign and seal of one's covenant relationship with God. Water baptism is the New Testament representation of the same thing.

You appear to assume that Holy Spirit baptism must precede water baptism, but you'll get an argument from those of us who practice covenant baptism as well as believer's baptism.

But the "one baptism" in 4:5 seems definitely to be a reference to physical (water) baptism because of its context in the rest of Paul's letter to the Ephesians.

-R