Down-firing Sub makes floor rattle

I think I've got some bad news for you. The vibrations that are being transmitted to your floor are more likely than not airborne, even that may seem counter intuitive. A down and dirty check - put your hand on the sub when its making the floor 'rattle' and see if the sub itself is producing a lot of vibrations. If not you might get some better help by shoring up the floor. JMHO.

Yes, it makes sense. You sub rolls off gradually above 39hz, your main speakers roll off gradually below 56hz, and the combined energy from both speakers between 39 and 56 hz will equal the out put on either speaker alone at the roll off frequency. BTW, this assumes that the crossover network you are talking about is the one built into the sub. An outboard crossover network not specifically made for your sub might have different slopes and require different frequencies.

Shadorne's point about other sources of rattle and ways to cure it is right on. I had a framed picture on the wall rattle and I wasn't even being overwhelmed by the bass. Thought it was in the electronics/speaker. Put some soft materiel between its bottom edge and the wall to fix it.

Flrnlamb is also correct about the sub's drivers position not being particularily relevant.