Coming to this a year after the fact (me and some friends are just starting up a Skull and Shackles campaign). The line about direct fire engines being more accurate is talking about the initial process of aiming them, i.e. it takes 0 rounds to aim and fire a light ballista, but it takes 2 rounds to aim a catapult. It is interesting to note that everything listed in Skull and Shackles that isn't a light ballista takes 2 rounds to aim, so they didn't really keep any kind of consistency with it anyway.
