Ideally, layout shifts would not be reported for content which shifted while within viewport but still completely obscured and not visible to users. (For example, when covered by a full screen overlay)
However, this is not currently the case, due to complexity and expense of computing if shifted nodes were actually fully obscured. I have gotten questions about this and found that there is no direct documentation in the spec, or the explainer.
Should we add a note to non-normative section or just to the Limitations section of explainer?