I think you will find you already had the answer in your PBO question with the extract from the Raymarine document. The longer shaft is used for heavier boat (much heavier than yours, I think at greater than 15 tonnes. As the table clearly shows it provides a greater stroke, more torque but a slower hardover time.
Anyway, rather than guessing why not just call Raymarine for advice. Pretty sure they will know which is appropriate.