This prescription is rooted in quantum mechanics which, despite its formal similarity, is physically very different from cosmology. The procedure looks innocent, but one should realize that there are already basic choices involved. Choosing the factor ordering is harmless, even though results can depend on it . More importantly, one has chosen the Schrödinger representation of the classical Poisson algebra, which immediately implies the familiar properties of operators such as the scale factor with a continuous spectrum. There are inequivalent representations with different properties, and it is not clear that this representation, which works well in quantum mechanics, is also correct for quantum cosmology. In fact, quantum mechanics is not very sensitive to the representation chosen  and one can use the most convenient one. This is the case because energies and thus oscillation lengths of wave functions described usually by quantum mechanics span only a limited range. Results can then be reproduced to arbitrary accuracy in any representation. Quantum cosmology, in contrast, has to deal with potentially infinitely high matter energies, leading to small oscillation lengths of wave functions, such that the issue of quantum representations becomes essential.
That the Wheeler-DeWitt representation may not be the right choice is also indicated by the fact that its scale factor operator has a continuous spectrum, while quantum geometry which is a well-defined quantization of the full theory, implies discrete volume spectra. Indeed, the Wheeler-DeWitt quantization of full gravity exists only formally, and its application to quantum cosmology simply quantizes the classically reduced isotropic system. This is much easier, and also more ambiguous, and leaves open many consistency considerations. It would be more reliable to start with the full quantization and introduce the symmetries there, or at least follow the same constructions of the full theory in a reduced model. If this is done, it turns out that indeed we obtain a quantum representation inequivalent to the Wheeler-DeWitt representation, with strong implications in high energy regimes. In particular, just as the full theory such a quantization has a volume or operator with a discrete spectrum, as derived in Section 5.2.
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