Our cover is a Coverstar autocover with an underguide system. The track is about 2" above the water, and the cover sits down on the surface of the water. So yes, it touches the pool.
I was able to get <1ppm loss overnight with the cover closed. But it seemed like the pool was looking really good for a couple of days before that. So I wondered if the cover may have been contributing to FC loss. In the end, if I extended the SLAM a couple of days, that is not all bad anyway.