Well, got my car back last night, looks like I could have been wrong. They claim the water in the footwell was coming from a pinched sunroof drain line, not condensate from the A/C system. I asked them if they shared a common drain and if that water could have backed up into the A/C/heater box, since I distinctly heard the fan picking up water. He said that's possible, since he thought the sunroof drain runs through the same area. He said be thankful the water overflowed into the footwell. If it had been blocked further up it most likely would have leaked from around the sunroof itself and I may have had to have a whole new headliner put in the car.
Anyway, I'm not 100% convinced it's fixed yet, they seemed a little fuzzy on knowing exactly what drains ran where under there. I ran the A/C last night and no problems yet, but I also didn't notice any water in the footwell the day before it went into the dealer, when I washed the car. One would think if the line was still blocked at that time the water from the hose would have caused it to leak into the footwell again. See what happens the next heavy rain we get.