There is nothing absolutely specific in the Westminster Confession about Roman Catholic baptism. What there is supports its validity. However there was a long-established acceptance of baptism by Roman Catholic priests, even more than by laymen or even women, and the Westminster Confession says nothing against it.
Perhaps more significantly, actions speak louder than words, or, in this case, inactions speak louder than words. From the earliest days of the Reformation there was never any tradition or practice of re-baptising those baptised by Roman priests. Luther, Calvin, Cranmer and Knox never doubted the validity of their baptisms. Only the Anabaptists practiced re-baptism (so-called, though they did not see it as such) and that was due to the objection to infant baptism and/or non-immersion.
The Westminster Confession (28 vii) states:
The Sacrament of baptism is but once to be administered to any person.
One could argue that if the first "baptism" was not valid, then a "re-baptism" would be the only baptism, which is what the Anabaptists did argue. Given the Westminster Divines opposition to anabaptism however, this is best interpreted as referrring to repetition of any form of baptism. Given that earlier genertions acceptd Roman Catholic baptism we would need something very specific to infer that the Westminster divines did not.
But doesn't the mere fact of being agents of the Antichrist disqualify them as lawful ministers of the Church? The Westminster Confession 25 vi, quoted by OP says:
There is no other head of the Church but the Lord Jesus Christ. Nor can the Pope of Rome, in any sense, be head thereof; but is that Antichrist, that man of sin, and son of perdition, that exalts himself, in the Church, against Christ and all that is called God.
Here we see that the Pope, though exaltng himself against Christ, is neverthless in His Church. The Antichrist is within, not outwith, the Church.
Samuel Rutherford, a Scottish representative to the Westminster Assembly, argued that Roman Catholic priests were valid ministers, in part from the premise that they had valid Baptism. The Church of Scotland was concerned at the rise of Independents and Separatists and Rutherford's wider strategy was to oppose the idea that anyone could be a minister without official endorsement. He did not accept baptism by laymen and argued from the general acceptance of Roman baptism the validity of Roman ministry. For the purposes of this question the point is that the validity of Roman Catholic baptism was so generaly accepted that it could be the basis of an argument. The Separatists claim was if they can do it so can we.
Two distinct views can be identified. One is that the Roman Catholic priests were de facto lawful shepherds of Christ's flock, however misguided or corrupt, and that their baptism was correct in the Trinitaran formula and the use of water, and so valid. Parallels were drawn with Caiphas, or with the scribes and pharisees who, sitting in Moses seat (Matthew 23 v2) should be heard. Also in the days of Hezekiah, nobody was re-circumcised.
The other view was the postman argument. Just as a letter, signed, sealed and posted, might be delivered by an official messnger, or dropped in the street and delivered by anybody, so it did not matter who perfomed the baptism, it came from Jesus Christ, with His seal.
Either way, whether because RC priests were valid ministers, or because it did not matter, Roman Catholic baptism was certainly valid; and the Antichrist was within the visible Church.
The validity of Roman Catholc baptism, from a Reformed perspectve, was an issue in Peru in 2004, and this anthology shows how the Reformed tradition has almost always acceped it. It includes etracts from the French Confession, Calvin, Knox, Beza, Perkins, Rutherford, Westminster, and others.
