Yup, set it the way you like it. My space shuttle came with all of its original card inserts for the apron. What I learned from that was that the manufacturers not only expected that there would be differences in ball count setup but also in reply score level and what the replay would be (extra ball or credit).
I sometimes switch my machines to 5 ball when having parties for novice friendly reasons described above. For personal play or playing with a skilled friend I prefer the challenge of 3 ball.