This study discusses the exploitation of a full-3D methodology for the electromagnetic simulation of a Wafer-Level Packaging solution featuring Through Silicon Vias (TSVs) for the redistribution of electrical signal from the in-package (RF-MEMS) passive devices to the external world. In particular, the Finite Element Method full-3D model is parameterised and allows analysing the influence of the most relevant Degrees of Freedom (DoFs) available in the package design, on the RF characteristics of encapsulated RF-MEMS passive devices. A previous part of this work, already published, discussed the validation of the mentioned full-3D model, comparing the results of simulations against experimental S-parameters datasets for a certain variety of Coplanar Waveguide test structures, in a frequency range from 50 MHz up to 30 GHz. Such a comparison showed good accuracy in predicting the behaviour of physical devices. Therefore, the soundness of the optimisation approach can be regarded as proven and consolidated for the optimisation purposes of the current work.