Why did the scholars overlook the inclusion of وقف (pausal marks) in specific instances—such as "لا إله إلا الله" (there is no god but Allah), "النبوة" (prophethood), and "لن تنالوا البر" (you will not attain righteousness)—which do not tolerate any alternative interpretations, while they affirmed them in other places?

The scholars did not place the "do not stop" sign on examples where stopping is clearly abominable. The scholarly efforts regarding stop signs vary and are not legally binding unless the reader intentionally stops or starts in a way that corrupts the meaning. As Al-Suyuti and Ibn Al-Jazari explained, the impermissibility of stopping refers to performance-related permissibility for improving recitation, not a prohibition, unless the intention is to distort the Qur'an and alter its meaning, in which case it is disbelief.