With OEM control arms, for optimal geometry I would suggest that the car's static height is no lower than 110mm of ground clearance at the front (picture 1, 2) and 120mm at the rear (picture 3, 4). With such set static height, even during suspension travel the geometry stays OK (track width, roll center, camber gain), unless completely bottoming out and you keep at least some minimum chassis rake that prevents the car from catching "boat gliding" effect by lifting front and squatting rear end and catching the air underneath. The softer the car, the bigger the problem of geometry and rake.
I have a bit more positive rake on my car with 100mm of ground clearance at front and 125mm at the rear due to increased rear downforce we are planning to run. With GMS front control arms the front end static height should be set with at least 95mm of ground clearance, while the rear end shall be at least 10mm higher to keep positive rake and should be increased accordingly on cars with increased rear downforce.
From geometry perspective, the rear static height should be set at minimum of 100mm of ground clearance which is quite low, but with such a low ride height at the rear you would need a front ride height set at 90mm to maintain at least minimum positive rake. But as mentioned above, with OEM front control arms you are out of its optimal geometry range already with any front ride height under 110mm.
The side skirt to ground clearance should be just an orientation as the panel gaps, tolerances, tire size and grounds are not valid measuring reference. On my car there is about 4-6mm of difference left/right if measuring from the side skirt to the ground. I strongly suggest to set the car by measuring the threads on the coilovers and using side skirt to ground clearance just for a first reference when you start to adjust the ride height. Don't forget to load the car (fuel, driver) as stock 4C with base suspension tends to sit quite a bit.
I'm off to alignment and corner balance rig on Friday, so I'll report more on that later...