We extend the multi-reference covariant density functional theory (MR-CDFT) by including fluctuations in quadrupole deformations and average isovector pairing gaps simultaneously for the nuclear matrix elements (NMEs) of neutrinoless double-beta decay in the candidate nuclei Ge, Se, Mo, Te, and Xe assuming the exchange of either light or heavy neutrinos. The results indicate a linear correlation between the predicted NMEs and the isovector pairing strengths, as well as the excitation energies of and states. By adjusting the pairing strengths based on the excitation energies of the states, we calculate the NMEs for decay, which are reduced by approximately to compared to the results obtained in the previous studies by Song et al. [Phys. Rev. C95, 024305 (2017)]. Additionally, upon introducing the average isovector pairing gap as an additional generator coordinate in the calculation, the NMEs increase by a factor ranging from to .

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