I suppose one might quibble on what it means to hold or not hold to the 1646 Confession (zero caveats allowed?) but the RPCNA holds to the 1646 and amplifies or clarifies with the testimony in a parallel column. I like this approach as it makes it clear where there are differences with the original confession and there are three:
1. The laws of consanguinity, WCF 24:4:
The RPCNA rejects the sentence "The man may not marry any of his wife's kindred nearer in blood than he may of his own; nor the woman of her husband's kindred nearer in blood than of her own" commenting that this prohibition is not warranted by Scripture.
2. The Pope as the Antichrist, WCF 25:6:
The RPCNA caveats this by testifying "Many antichrists will be present in the world throughout history. Prior to Christ's coming the final 'man of lawlessness' will be revealed. He will be destroyed by Christ."
The two above I would say are fairly minor. The more significant one is this:
3. Portions of the establishment principle. WCF 23:3 states:
"The civil magistrate may not assume to himself the administration of the Word and sacraments, or the power of the keys of the kingdom of heaven: yet he hath authority, and it is his duty, to take order, that unity and peace be preserved in the Church, that the truth of God be kept pure and entire; that all blasphemies and heresies be suppressed; all corruptions and abuses in worship and discipline prevented or reformed; and all the ordinances of God duly settled, administered and observed. For the better effecting whereof, he hath power to call synods, to be present at them, and to provide, that whatsoever is transacted in them be according to the mind of God."
The RPCNA rejects the crossed out portion, but comments:
"Both the government of the nation and the government of the visible church are established by God. Though distinct and independent of each other, they both owe supreme allegiance to Jesus Christ. The governments of church and state differ in in sphere of authority in that due submission to the government of the visible church is the obligation of members thereof, while due submission to civil government is the obligation of all men. The governments of church and state also have different functions and prerogatives in the advancement of the Kingdom of God. The means of enforcement of the civil government are physical, while those of church government are not. Neither government has the right to invade or assume the authority of the other. They should cooperate to the honor and glory of God, while maintaining their separate jurisdictions."
So it does not deny that the magistrate is to further the kingdom of God, but clarifies the spheres where each have authority. The state should strive to keep purity in the state and the church should strive to keep purity in the church. It goes on to say:
"Though responsible for maintaining conditions favorable to the spread of the Gospel, civil government should never attempt to convert men to Christ by the user of force or by persecution. It should guarantee to all its subjects every human right given by God to men. It should, however, restrain and punish its subjects for those sinful actions which fall under its jurisdiction."
The testimony's stance seems pretty reasonable to me and the concern over it being different from the 1646 seem out of proportion to reality.