There is an ongoing quest to improve on the spectroscopic quality of nuclear energy density functionals (EDFs) of the Skyrme type through extensions of its traditional form. One direction for such activities is the inclusion of terms of higher order in gradients in the EDF. We report on exploratory symmetry-breaking calculations performed for an extension of the Skyrme EDF that includes central terms with four gradients at next-to-next-to-leading order (N2LO) and for which the high-quality parametrization SN2LO1 has been constructed recently [P. Becker et al, Phys. Rev. C 96, 044330 (2017)]. Up to now, the investigation of such functionals with higher-order terms was limited to infinite matter and spherically symmetric configurations of singly- and doubly-magic nuclei. We address here nuclei and phenomena that require us to consider axial and non-axial deformation, both for reflection-symmetric and also reflection-asymmetric shapes, as well as the breaking of time-reversal invariance. Achieving these calculations demanded a number of formal developments. These all resulted from the formulation of the N2LO EDF requiring the introduction of new local densities with additional gradients that are not present in the EDF at NLO. Their choice is not unique, but can differ in the way the gradients are coupled. While designing a numerical implementation of N2LO EDFs in Cartesian 3d coordinate-space representation, we have developed a novel definition and a new unifying notation for normal and pair densities that contain gradients at arbitrary order. The resulting scheme resolves several issues with some of the choices that have been made for local densities in the past, in particular when breaking time-reversal symmetry. Guided by general practical considerations, we propose an alternative form of the N2LO contribution to the Skyrme EDF that is built from a different set of densities.