You can't change a check box's colour using conditional formatting.
But if you were REALLY desperate you could put every checkbox inside of a section and make the section background colour conditional formatting.
You can use a single group node/field in your datasource - you don't have to have one for every check box.
When you make the section, set all it's margins, padding and borders to zero. That will give you the closest fit to the checkbox control.
But you know, only if you are desperate. Example attached.