Because Trent reiterates "as it is written; unless a man be born again of water and the Holy Ghost, he cannot enter into the Kingdom of God." And also because the majority of the early fathers held to water baptism, and St. Gregory nαzιanzus denies it.
Finally, corrupt fruits only come from a corrupt tree. The fruits of BoD is seen in V2 and salvation outside the church.....
Yes, John 3:5 and other Scripture must be wholly rejected, forgotten, and ignored and the thrice defined dogma denied for the idea of a BOD to be a doctrine of the Church or anything more than theological speculation.