I just saw your original question, and someone already answered it! I believe they didn’t include them because the 60th Anniversary Jazz isn’t a direct copy of the original stack-knob Jazz. Similar to the 50th Anniversary Jazz bass, it’s an amalgamation of the early Jazz Bass years. It has a nitro lacquer body (although in a current color of the Ultra line rather than an original color), stack-knobs, ashtray covers, reverse tuners, 7.25” fretboard radius, along with the transitional “bound and dot” fretboard (only available for a short time in 1966, I believe, before becoming bound with inlay). So to me it makes sense that the original style mutes weren’t included, although I do think it would have been a cool case-included addition. It would have been nice if Fender included the muting foam that used to be installed inside the bridge ashtray, but they didn’t do that, either! I can’t speak on the Custom Shop models, however, as I’ve never owned one! I personally think it would have been neat if the 60th Anniversary also came with 70’s bridge pickup location, which I think would have given a unique sound with the stack-knobs and 62 pickups. Maybe for the 70th Anniversary model.....