We discuss gauge theories of scale invariance beyond the Standard Model (SM) and Einstein gravity. We show that the non-metricity of their underlying 4D geometry is at the origin of mass generation and discuss phenomenological implications. Examples of such theories are Weyl's original quadratic gravity theory and its Palatini formulation. Non-metricity leads to spontaneous breaking of this gauged scale symmetry to Einstein gravity. All mass scales: the Planck scale, the cosmological constant and the mass (m ω ) of the Weyl gauge boson of scale symmetry (ω µ ) are proportional to a scalar field vev that has a (non-metric) geometric origin, in the R2 term. With ω µ of geometric origin, the SM Higgs field has a (non-metric) geometric origin too, being generated by Weyl boson fusion in the early Universe. This appears as a microscopic realisation of "matter creation from geometry" discussed in the thermodynamics of open systems applied to cosmology. Unlike in a locally scale invariant theory (no ω µ present) with an underlying (metric) pseudo-Riemannian geometry, here there are no ghost degrees of freedom or additional fields beyond the SM and their underlying Weyl/Palatini geometry, the cosmological constant is predicted positive and their connection shares the symmetry of the action. An intuitive picture of non-metricity in solid state physics is also provided, where it is associated with point defects (metric anomalies) of the crystalline structure.