How is the CR calculation affected by spell slots?

@Hilgefka @JeremyECrawfordHow (if at all) is the CR calculation affected by spell slots (e.g., 2 third level slots for a Flameskull)? the spell design advice shows the damage a spell is worth based on its level. Use that to determine offensive CR

— (((Mike Mearls))) (@mikemearls) June 25, 2016