Or is it because the crossover point between the subs and tops is lower with Funktion One, allowing the F221 to focus more energy on the lows and thus sound deeper?
This is a very common thing-to make a sub "appear" to have more low end-just roll of more top end-or crossover lower.
Since the higher freq are louder-when you have less of them to "get in the way", the bass sounds lower.
There is one manufacturer who uses this "technique" to give what call (not their term here) Extended bass response. When in this "mode" the low end response is the same-but they just roll of the highs-so it "sounds" lower. Fools a lot of people however. And people "think" that this mode gives them more bass-when all it is really doing is less highs.
I have no idea or opinion on your particular case, but it is something to consider.