Gene regulatory networks can be modelled as nonlinear dynamical systems whose trajectories encode sequences of gene expression directing biological programmes. Function is determined by the geometry of these trajectories in phase space, which specifies the ordered progression of gene states required for correct developmental outcomes (such as patterning or limb formation). Closely related networks may share similar geometric structure while exhibiting different temporal behaviour, giving rise to distinct functional timescales defined by transient dynamics such as oscillation periods or relaxation times rather than steady states. Parameter perturbations typically affect geometry and timing in coupled and unpredictable ways, complicating comparison between systems and targeted modulation of tempo. We introduce a framework that characterises functionality via equivalence classes of orbits, inducing a distance between parametrised systems that separates temporal reparameterisation from geometric deformation. This enables identification of parameter directions that modulate functional timescale while preserving the underlying dynamical landscape.