The suggestion of bad hubs isn't entirely off base from what I've read (pistons get pushed back by the rotor wobbling, so you end up with free play in the pedal extending the pistons back out until the pads meet the rotors) but you'd only have the problem while the car was moving, and then it would pump back up after a few strokes.
The Pathy brake booster I had apart did not have a solid rod from input to output, but the two rods met in the middle and should give a solid pedal whether the diaphragm is working or not. The slop between the two rods is what opens and closes the valve that controls air pressure against the back of the diaphragm in the booster. But no, unless the booster went entirely to pieces inside, a failed booster should not allow the pedal to go to the floor. (I replaced mine thinking it was the only thing left that could be wrong, and it solved nothing.) I'd be hesitant to say the new MC didn't do it without bleeding the thing first, even though it sounds like you were careful with it. I'd also be suspicious of the ABS system.
After the fun I had last summer with mine, I hate brakes. There's no telling what's wrong unless it's leaking, or where the air is, or if there's air, or whether the new part or the bleed was what changed something.