If you change line 112 in UIAtlasMaker.GetSelectedTextures from
Object[] objects = EditorUtility.CollectDependencies(Selection.objects);
to
Object[] objects
= Selection
.GetFiltered(typeof(Texture
), SelectionMode
.DeepAssets);
you can now add all the sprites in a subfolder to your atlas, rather than having to select them individually.
Do bear in mind, that if you have duplicates, it will "crash" the atlasmaker window, so don't select root. This is the same behavior as is now, if you select two sprites with the same name, so not a big deal though.