Both the Council of Florence and the Council of Trent neither taught what St. Thomas had speculated on BoD and BoB, nor explicitly condemned it. I think that's because the speculations of St. Thomas were neither based on revelation, nor on a common teaching of the Fathers. Neither divinely revealed, nor in a solid way based on tradition.
Both Councils weren't concerned with sorting out the ideas of Catholic theologians. They had other tasks. The Council of Trent implicity rejects BoD and BoB, by naming several necessary conditions for justification. These include the laver of generation, voto, preparation, faith, and more. The candidate asks the Church for the faith, and receives infused that sort of faith, hope, and charity, without which none can please the Lord.
Why didn't they explicitly condemn BoD and BoB? Why did they only strictly forbid to teach, preach, or believe anything else on justification? The Lord knows why. However, a replacement for the sacrament of baptism is neither divinely revealed, nor consistently found in tradition.