I modified your topic title to refer to the taxon page, since atlases use a different map format as far as what displays at different zoom levels. (Mostly for others reading this) There is a description about some of the differences between taxon page maps and atlases here: https://www.inaturalist.org/pages/atlases
I’m not sure I understand, since that is what I am seeing for your examples, Austruca variegata and Minuca pugnax
Green polygons are regions where there are research grade observations associated with the listed taxon in that place. Orange polygons are where the taxon is on a checklist for that place, but there are no research grade observations for that place.
Coarsest zoom:
Countries
Intermediate zoom:
Countries explode into regions; countries with no RG observations disappear
Finest zoom:
Regions explode into districts; regions with no RG observations disappear
Is your preference to always display the orange checklist countries and regions at the finer zooms?