We consider the impact of multi-parton interactions and colour reconnection on the modeling of vector boson fusion and vector boson scattering (VBS) final states at the Large Hadron Collider (LHC). We investigate how the variation of the model parameters, compatible with a reasonable spread of predictions around typical tuning observables, extrapolates into the VBS phase space. We study the implications of this variation on the total uncertainty budget attached to realistic simulations of the final states in current event generator predictions. We find that the variations have a non-trivial phase space dependence and become comparable in size to the perturbative uncertainties once next-to-leading order predictions are combined with parton shower evolution.