Calvin did not think a new Confession needed to be written for the churches in the Low Countries, but he did not oppose or condemn it in anyway. It appears that he simply thought the French Confession of 1559 was good enough for the Low Countries as well. Yet, the ministers in the Low Countries seemed to disagree. Perhaps because the situation had radically changed between 1559 and 1561. Geneva was a relative safe spot for the Reformation and Calvin did not experience there any real persecution from the Romanists. This was not the case in Belgium. Even France, which used Calvin's Confession of 1559, was relatively peaceful in that year. But by 1561 persecution had really broken out across France and the first wars of religion were being fought. In 1559 the Colloquy at Poissy was on the horizon and hope for a peaceful settlement still existed. But in 1561, France had seen the Massacre at Vassy, and the beginning of never ending strife had started. The Low Countries were even worse. The Inquisition was occurring and the ministers in the Low Countries often fled into France for safety telling you something about how unsafe the Low Countries really were for Reformed believers. I think that this attitude can be found in the Belgic Confession. Let us compare the French Confession of Calvin in 1559 to the Belgic and how it speaks of the Roman Catholic Church.
As a note, I will be using the French Confession as translated by William Foote in The Huguenots (1870), and the Belgic Confession the Christians Reformed Church 1976 Psalter edition as reprinted in Reformed Confessions of the 16th and 17th Centuries Vol. 2 by James Dennison.
The French Confession speaks directly about the Roman Church in Article 28:
"In this belief we protest that when the Word of God is not received and when there is no professed subjection to it, and where there is no use of the sacrament, if we will speak properly, we cannot judge that there is any church. Wherefore we condemn those assemblies in the papacy, because the pure Word of God is banished out of them, and because in them the sacraments are corrupted, counterfeited, falsified or utterly abolished, and because among them, separate and cut themselves off from the body of Christ Jesus. Yet nevertheless, because there is yet some small track of a church in the papacy, and that baptism as it is in the substance, has been still continued, and because the efficacy of baptism does not depend upon him who administers it, we confess that they which are thus baptized do not need a second baptism. In the meanwhile, because of those corruptions which are mingled with the administration of that sacrament, no man can present his children to be baptized in that church without polluting his conscience."
The Belgic goes head on wit the Roman Church in Article 29. I will start with paragraph 2.
"The marks by which the true church is known are these: If the pure doctrine of the gospel is preached therein; if it is maintains the pure administration of the sacraments as instituted by Christ; if church discipline is exercised in punishing of sin; in short, if all things are managed according to the pure Word of God, all things contrary thereto rejected, and Jesus Christ acknowledged as the only Head of the church. Hereby the true Church may certainly be known, from which no man has a right to separate himself.
With respect to those who are members of the Church, they may be known by the marks of Christians; namely, by faith, and when having received Jesus Christ the only savior, they avoid sin, follow after righteousness, love the true God and their neighbor, neither turn aside to the right or the left, crucify the flesh with the works thereof. But this is not to be understood as if there did not remain in them great infirmities; but they fight against them through the Spirit all the days of their life, continually taking their refuge in the blood, death passion, and obedience of our Lord Jesus Christ, in whom they have remission of sins, through faith in Him.
As for the false Church, it ascribes more power and authority to itself and its ordinances than to the Word of God, and will not submit itself to the yoke of Christ. Neither does it administer the sacraments as appointed by Christ in His Word, but adds to and takes from them, as it thinks proper; it relies more upon men than upon Christ; and persecutes those who live holily according to the Word of God and rebuke it for its errors, covetousness, and idolatry.
These two Churches are easily known and distinguished from each other."
I think an interesting difference in tone more than in substance takes place here. Calvin in the French Confession does make sure to point out that certain assemblies in the papacy banish God's Word, and corrupt the sacraments, but he then goes out of his way to speak about a small track of the church in the papacy, and how there is no need for rebaptism in what seems like perhaps a precaution against Anabaptists or other extreme reformed movements.
The Belgic on the other hand seems to speak in harsher terms about the Roman Catholics. Pointing out directly that the church lowers Jesus Christ putting more faith in man than in the Savior. Refusing to submit to Christ they go a step further and "persecute" those who do submit to that yoke of Jesus Christ. The papacy is condemned outright by making a mark of the true church acknowledging Jesus Christ as the lone head of the church. The Belgic puts a contrast forth that the true Church (the Reformed churches) follow Christ in all things, and the Roman Church rejects Christ and puts more faith in man's power and authority. This is the basis for rejecting Rome as a true church. There is no thought of dangers of Anabaptists or other extremists Protestant groups, but rather the Belgic focuses in on the extreme danger of Roman Catholicism.
Note also the call for people to leave the Roman Catholic Church found in the Belgic. In discussing the true church the Belgic states, "from which no man has a right to separate himself". And with the false church of Rome, "The two churches are easily known and distinguished from each other." In other words, if you are a believer in Jesus Christ, a Christian, you ought to be able to see the difference between the false church of Rome and the true Church, which is persecuted. And there is no reason whatsoever for you not to leave the Roman Church and join the Reformed Church. You can easily know the difference and you have no right to remain separate from a true church. It is true that the French Confession speaks of a polluted conscience if one stays within the Roman Communion, but the French Confession also admits a "small track of a church in the papacy". That is something the persecuted church in the Low Countries does not place in their confession.
The Belgic Confession draws a sharper contrast between Rome and the Reformation and that contrast is based on Christ. One church submits and follows Him, and the other rejects and persecutes Him. This is something that runs throughout the Belgic Confession, as we shall see.