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A bass reflex port works essentially the same regardless of where on the enclosure it is mounted. However if the port is very near a boundary such as a wall or floor, then that certainly changes the equation. How close is your down firing port to the floor?
The frequencies that come out of the port are omnidirectional, so it doesn't really matter which side of the enclosure they're on. However, it is important to give the port some distance between it and a nearby boundary (A good rule of thumb is approx the diameter of the port) If you get too close, it will impede the port and the enclosure will act something like a sealed or aperiodic enclosure.
Isn't it about time we started answering rhetorical questions?
There does seem to be something happening when a down firing port is empirically placed a specific distance from the floor, a type of loading occurs. Adds to the mass in the port? I know it may go against common practice, but apparently you can utilize the floor (boundary) to enhance the bass. I don't know all of it, bit I've seen it done. The Wolcott Audio Omnispheres had 3 large down firing ports per the usual calculations, however Mr. Wolcott arrived at an optimal height off of the floor with microphone tests.