It's the EPiServer.Web.WebControls.InputEditorOptions that renders the checkboxes.
It does a foreach on the EditoToolOption enum. I guess you could try making your own implementation overrideing the CreateChildControls. Then either use it directly in the Admin\EditPageTypeField.aspx or make your own version and use virtualpathmappings to use your version.
Or make your own version of EditPageTypefield override the onload and use virtualpathmappings to use your version. it's in the onload that the hiding/display of the editoroptioncheckboxes are made.