Is it permissible to prevent students and teachers from wearing transparent niqabs or those with two layers, especially since students intentionally uncover these coverings after leaving school or while riding transportation?

The khimar does not have to be multi-layered. The obligation is to cover the face, whether with one layer or more. The khimar and niqab are permissible. It is obligatory to adhere to the Shari'ah in the description of the khimar or niqab. Therefore, it is not permissible to widen the openings of the niqab beyond the eye area, nor is it permissible for the khimar to be transparent. The responsibility of the Quranic memorization center is to ensure that the teachers and students adhere to the obligatory covering inside the center. What happens outside is not its responsibility except through advice and guidance.