I'm just fitting the uprated front springs to my restored struts and noticing they are 5mm narrower on the big diameter so they sit away from the cup edges, the originals fit snuggly and even were quite worn flat. Also annoying my spring compressors chipped the nice new paint on the cups as there was not enough clearance.

Do the springs diameters provide any geometry to the suspension or is all done by the shock? Will I damage my shock?

The damper (and the rest of the suspension components) will act in the same manner regardless of spring dia.

Coilovers generally come with springs in 1.9/2.25/2.5" diameters and operate just like the standard parts they replace if the standard pickup points are maintained

The spring diameter does effect the characteristics of the spring. The biggest problem with coilovers is the loading on the damper is no longer even