Well, a lot of these tasks are already automated (ie, shakers), but most bench workers have their own quirks on existing protocols. Most labs have their own 'dialect' of common mol bio techniques that 'work' in their particular setup. Perhaps the reagent from their particular supplier requires a longer incubation time, or the enzymes are wonky and you need to add more. Everybody I know does washing steps their own way - they say the "official" protocol is too long/cumerbersome/wasteful. More often than not, their own variant of the protocol is documented in their lab books, but not in the publications, where it cites the original protocol.