EFSS has experienced workers marking their harnesses and lanyards for decades. Only part of the webbings is involved and EFSS never has seen any consequences to this practice. However, manufacturers of permanent markers do not make the contents clear  althugh we can assume they include a solvent that should not harm polyester and an insoluble organic and perhaps inorganic colored powder that sits on the surface and resists uv. The effect of sun or uv is an unknown on any two chemicals until a reliable repeat test is done; you could do this perhaps and measure change in strength after a summer in the sun or even a year or two.
Various committees in fall protection come up with this question every few years. Nothing is resolved as I recall. In face of the unknown, manufacturers are going to take the position of advising against it. However it is an easy identifier for workers to claim identification with three initials as opposed to tags which can fall off or become defaced.
Maybe spray parts of harness straps that are an excess for the user or the back of the shock absorber section or even the snaps, as a lost cost way around the problem.