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Fluctuations play an important role in diffractive production of vector mesons. It was in particular recently suggested, based on the Impact-Parameter dependent Saturation model (IPSat), that geometrical fluctuations triggered by the motion of the constituent quarks within the protons could explain incoherent diffractive processes observed at HERA. We propose a variant of the IPSat model which includes spatial and symmetry correlations between constituent quarks, thereby reducing the number of parameters needed to describe diffractive vector meson production to a single one, the size of the gluon cloud around each valence quark. The application to $J/\Psi$, $\rho$ and $\phi$ diffractive electron and photon production cross sections reveal the important role of geometrical fluctuations in incoherent channels, while other sources of fluctuations are needed to fully account for electroproduction of light mesons, as well as photo production of $J/\Psi$ mesons at small momentum transfer., Comment: 17 pages, 15 figures, major revision, title changed, new sections included , figures added to discuss vector meson electroproduction, new references, version accepted for publication in EPJ C