I can think of two possible causes for your problem. One would be debris (leaves, pine needles, stuff like that) blocking the water drains that are just below the base of the windshield, and the other would be a plugged drainline from the sunroof.
I'm not sure if you want to investigate the problem yourself, or take the car to your VW dealer. It's 50/50 whether or not debris under the hood would be considered a 'warranty' issue or not, so, you might be better off to do a little investigation on your own first. Here's a quick how-to:
Cabin Air Intake Plenum
Air is drawn into the heating and cooling system for delivery to the cabin via the large hole that you can see in the first picture below. This is the hole in the middle of the car, directly behind the engine. That hole has (or should have) a neoprene gasket all around it, very similar to the door gaskets. If that gasket is missing, then you have found your problem.
If that gasket is there and it does not appear to be damaged, have a look at the areas on either side of it. See if there is any debris present on top of the black plastic covers. If the top of the covers are both clear, remove the cover (it is fairly easy to do) and inspect underneath. If you have a garden hose handy, run water into either side of the area directly in front of the windshield - but don't run water into the air intake hole in the middle! See if the water runs out freely - it should drain out onto the ground pretty quickly.
While you are in there, have a look at the two pollen filters that are mounted on the underside of the hood - check and see if they are wet. If they are wet, that is pretty good evidence that water is pooling up in the areas on either side of the central air intake.
Cabin Air Intake
If everything appears clean on first inspection, remove the large plastic cover that runs across the back of the engine compartment, over top of the cabin air intake. I have posted instructions below. The 'trick' to removing this cover is to first unlock the four fasteners, then lift the FRONT edge of the cover, then pull the cover forward about an inch as you lift it up.
There is also a fully illustrated post explaining how to remove the plenum chamber cover here: How to remove the Plenum Chamber Cover
Removing the debris screen
Twist the four fasteners a quarter of a turn each
Example of Debris under the Cover - in this case, pine needles
It helps to know where the retaining hooks on the bottom of the debris screen (shown above) are before you try to remove it.
Once you have removed this cover, inspect for debris in the wells on either side of the cabin air intake (the middle hole). Perhaps try adding water to the side wells with a garden hose, and observing under the car to see if it is flowing out at an acceptable rate of speed. At the same time, inspect the second gasket that seals the bottom of the debris screen to the perimeter of the cabin air inlet (in the middle of the car) to make sure there are no problems with it.
When you re-install the debris screen, pay attention to how you arrange the rubber flaps at each end - this matters. Note how the rubber flaps fit OVER the big cover, as seen in the photo at the very top. Also, be aware that the raised lip on the aft edge of the debris screen fits under the cover that is attached to the base of the windshield. It is fiddley work to get the cover re-installed, so, take your time and take it easy. There is a way to get it in there without force - it just isn't obvious, that's all.
If you have not discovered any problems in the air intake area, then the source of your leak is likely one of the drain tubes that run from the sunroof down to the bottom of the car. There are four drain tubes in total, one in each corner of the sunroof assembly. They run down the two front A pillars and exit just behind the front wheels, and also run down the two rear C pillars and exit into the upper wheel well area, behind the rear wheel well liners.
Three things can (commonly) go wrong with these drain tubes on any car that has a sunroof:
1) Tube opening gets plugged by debris up at the sunroof itself.
2) Tube comes apart somewhere between where it leaves the sunroof and where it exits the bottom of the car.
3) Opening on the bottom of the car gets blocked, so water backs up the tube and leaks out a joint somewhere.
I have no experience troubleshooting sunroof leaks. The best suggestion I can offer is to open the sunroof glass fully, then get a watering can with a narrow spout and pour water into each side of the sunroof frame assembly, outboard of the hole in the headliner. In order to test all four outlets, you will probably have to find a hill somewhere and park the car nose down and nose up, to cause the water to run out the front and rear outlets on each side. However, if you are getting water infiltration into the front passenger footwell, that kind of suggests that there may be a problem with the front passenger corner tube.
I have posted an illustration below that shows the position and routing of the four water drain hoses in each corner of the Phaeton sunroof. Be aware that the rear two hoses drain from the very aft corners of the sunroof frame - in other words, about two inches outboard and to the rear of where the back of the glass panel will be when the sunroof is open. So, you won't be able to see the drain holes that lead to those two rear hoses when you look in from above... hence the need to do a function-check with a watering can.
My guess is that your problem will be found where I have put the red arrow in the illustration below... the hose has probably come out of the socket in the rubber piece that fits into the engine compartment bulkhead. Although it is fairly easy to get access to the outlet of the front two drain hoses (some further disassembly is required, which I do not recommend you try yourself due to the risk of breaking the windshield - see this post for full details: How to remove the Plenum Chamber Cover), it is a nuisance to get to the two rear outlets - you have to remove the rear wheel and then remove the rear wheel well liner. See the photos below for locations of the sunroof drain outlets.
Sunroof Drain Design Illustration
To clean the drain lines, you run a thin, flexible cable (a speedometer cable with a 2mm ball glued on the end is perfect) down the hoses from the sunroof - or, up the hoses from the drain hole, whichever is easier. However, if the tube has come apart from the grommet assembly where it passes through the firewall (front) or body structure (rear), cleaning won't fully solve the problem - you will need to do more disassembly of the interior of the car to get access to the rubber grommet that the drain tube terminates at, where it passes through the metal bulkhead. That level of disassembly is beyond the scope of this reply.
Hope this helps...
Location of Sunroof Water Drain - front of car
Location of Sunroof Water Drain - rear of car
This is an excellent picture for the purpose of showing how the drain hose mates with the grommet. The design is similar at the front. Slight disassembly is required to get access to this, although it is faster and easier to get access to the rear one.