Is there scholarly consensus on the impurity of what enters the urethra and then exits—such as water used for istinja' (ablution after defecation/urination) or from a swimming pool—and is the difference of opinion on this matter significant enough to allow adopting the view of those who consider it pure?

The affliction of obsessive doubts has no cure except by completely disregarding them, refraining from preoccupation with them, cutting off engagement with them, not asking about them, and supplicating to God to cure you of them. You should also consult psychiatrists. What you mentioned about water entering the urethra after ablution is nothing but a form of obsessive doubt, for it is apparent that it is residual water on the male organ from the ablution, and it is pure. The نقل (transmission) you cited from the book "Al-Muheet Al-Burhani" contains a concession regarding the purity of the ablution water exiting the male organ, and that it does not invalidate ablution.