We study the Fock quantization of scalar fields of Klein-Gordon type in nonstationary scenarios propagating in spacetimes with compact spatial sections, allowing for different field descriptions that are related by means of certain nonlocal linear canonical transformations that depend on time. More specifically, we consider transformations that do not mix eigenmodes of the Laplace-Beltrami operator, which are supposed to be dynamically decoupled. In addition, we assume that the canonical transformations admit an asymptotic expansion for large eigenvalues (in norm) of the Laplace-Beltrami operator in the form of a series of half integer powers. Canonical transformations of this kind are found in the study of scalar perturbations in inflationary cosmologies, relating for instance the physical degrees of freedom of these perturbations after gauge fixing with gauge invariant canonical pairs of Bardeen quantities. We characterize all possible transformations of this type and show that, independently of the initial field description, the combined criterion of requiring (i) invariance of the vacuum under the spatial symmetries and (ii) a unitary implementation of the dynamics, leads to a unique equivalence class of Fock quantizations, all of them related by unitary transformations. This conclusion provides even further robustness to the validity of the proposed criterion, completing the results that have already appeared in the literature about the uniqueness of the Fock quantization under changes of field description when one permits exclusively local time dependent canonical transformations that scale the field configuration.
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