In Chef Gui's cookbook, every time he refer to “whole grain” flour, it is meant to be whole grain wheat flour (sometimes referred to as “whole wheat”). He calls it whole grain because in Canada (where the cookbook is also sold), “whole wheat” doesn’t necessarily mean “whole grain”.
As a general rule, substituting flours 1-for-1 usually does NOT work well, unless it has been previously tested. And even so, success only happens through trial and error. Chef Gui recommends treading lightly when substituting flours.