No, the whole wheat berry isn’t just ground up and put into a sack, if that’s what you were thinking. OK, sure, it can be like that at some boutique low-production mills, but commercially speaking, whole wheat flour is made in exactly the same way regular white flour is made. The difference is that after the pure wheat endosperm is extracted and milled, ground and sifted brand and germ is mixed back into it, thus producing whole wheat flour.
Why? Part of the reason is because the bran and germ behave differently under the rollers compared to the endosperm. If all the various components of the wheat berry were processed together, none of them would be reduced to as fine a consistency as they would otherwise be if they were processed individually, and a fine consistency is important for lighter, finer-tasting breads.
Also, different flour makers have different ideas about what “wheat” flour is. For some it’s less than the full amount of germ and bran that came with the original wheat berries. For others it’s the full amount. I suppose for still others it could be even more, though I’ve never heard of a commercially-available flour like that. All of which goes to show that if you’re going to be a wheat flour buyer, it pays to know your millers.