Ok had this problem on my facelift estate. The water is getting in past the seal on what you describe as the cut out up under and behind the glove box. The cause, the drain grommet which takes the rainwater away is blocked. You can access this by lifting away the plastic mesh grill just in front of the bulkhead, the bit where the wiper arm spindle passes through (passenger side). You need a torch and you will be able to see down there where water collects and should drain away. Mine was like a mini water holding tank, it was blocked and stank awful, been blocked for ages. I think what fills it up quickly if blocked is very heavy rain, and we have had some of that recently. Just poke a stick or get your hand in there and remove the debris.
I had to remove all of my carpets front and rear on that side then cut away carefully the sound deadning material to let it dry out properly. Beware on the facelift there are parts of the wiring loom that run under this matting in the passenger footwell, be careful with that stanley knife if you choose to cut it away for drying, best to as it starts to stink after a while.
Not sure whether it's the same on pre facelift models. Anyway keep checking to keep it clear of debris in future, especially if you park near trees bushes etc like me, all the crap gets down into this area and blocks it over time.
Mick