When enabling any of the Core Search Facets, they filter the other search facets so that it searches those attributes only in the filtered subset. However, when enabling one of the Commerce Option Facets, it does not affect the other search facets. As a result, when you enable an option facet and then enable a Core Search facet, there's a strong chance your option facet will disappear in the intersection with both enabled. If you want to remove the option facet you enabled, you have to first uncheck the core search facet and then you can remove the option facet.
For example, as shown in the gif, when the "Home Page" category is enabled, the other facets are only searching on the remaining 3 matches. However, doing the same with an Option Facet first, the other facets are not affected and still display the numbers in the complete set of entries.