I tend to feel the unique signatures (Charlie Christian, Bonnamassa Amos) and weird innovative cross combos (things like P-90 in a Strat or Melody Maker cover, humbucker under Jazzmaster, or '53 tapped tele) those sound like legit Custom Shop...
....meanwhile the standard drop-in replacement pickup types that are variants of production pickups (RTM, Frankenstein, Hunter, Concept Set, Eclair) or pickups that already have sister/brother production variants (Pearly Gates for Tele, Pearly Gates for Strat - there's already JBjr and Lil'59 and a trembucker Pearly for Big Apple strat, etc.; why not have these Pearlies as production?), the latter feel like they should be production. Doesn't seem like that the latter require a special wind, special wire or special non-standdard components to make in order to require Custom Shop status. All Custom Shop does is delay receiving it.