In very heavy rain with the car parked on an incline, it is possible for the foam gaskets that surround the tailights to become saturated and allow rainwater into the trunk.

I know this because it happened to me. During the holidays when I was in Northern California, some very heavy storms came through. I only got about a 1/2 inch in the spare-tire well.

Given the large quantity of water described in your scenario, I also suspect one or more of the sunroof drain tubes may be clogged, leaking or otherwise damaged. The only real solution now is to strip the interior out and assess the level of damage.