Ilkka's charted the different EQ profiles of the 20, 16, and 12hz settings, and I'd have to imagine the center frequency of the highpass gets changed as well, maybe 18, 14, and 10hz (guesses). By keeping all three ports open, the enclosure is still physically tuned to 20hz, yet with the 16hz filter setting, a boost is being applied down low and the highpass is lowered to maybe 14hz, putting you at risk for potential bottoming with high output, low frequency material. If you don't play your media very loud, you'll be ok, it's not like you're hurting the driver, but you'll be losing some protection in the event that a demanding low frequency scene does come up. You have to assume they created the filter profiles for the tunes they did for a reason
What model do you have and how loud do you typically listen at?