Why would a recipe call for bone-in, skin-on chicken and then never use the bone/skin? This America's Test Kitchen recipe for Slow Cooker Chicken with "Roasted" Garlic Sauce 
has the ingredient:


  bone-in split chicken breasts, skin and ribs removed, trimmed of all visible fat


The skin and ribs are never used in the recipe.

ATK generally does a great job of simplifying recipes but needing to de-bone the chicken rather than simply buying boneless, skinless chicken breasts seems silly. Plus, I generally find bone-in, skin-on chicken breasts to be harder to find than boneless, skinless chicken.

I asked my butcher if there's a difference between them doing it and doing it myself and he said that there wasn't (assuming they're never used).

Is there something my butcher didn't think of?



Yes, I know that there's a cost difference but let's ignore that, as that's not generally a consideration in ATK recipes.
Bone in = the breast plate is still there.  The ribs would typically be removed because in slow cooking the rib bones often have a habit of coming loose and being an annoyance or even a choking hazard while adding little or nothing to the taste.  Leaving the breast plate however is referred to by many as cooking on the crown.  Cooking on the crown is considered by many to give a better flavor, be it poultry, beef, pork, or whatever.  Additional, with slow cooking, the cartilage and bone may add some thickening effect to your broth.