The drains by the battery allow the water to exit onto the fuel tank and out of the car .. if missing then it actually aids the removal of water .
The bungs are only really there to stop rodents entering the car .. trust me the little buggers get in other ways so they dont really serve a purpose.
Im dropping a 996TT engine tomorrow for rodent damage !
Its pretty common for them to be missing and unless you have a mouse problem where you park it then i wouldn,t recomend replaceing them .
Early 996 had a tube leading off from the drain bungs .. you cant replace these without major work and again without them it wont cause water to get into the car .
Couple of things im thinking here ..
The panels over the battery and either side are fitted ?
The pollen filter will have a foam cover over it , if missing water can drop onto the pollen filter and into the car via the heater system .
The foam seal under the pollen filter tray can cause a leak.
The foam seal behind the battery with the heater pipes going through it can come unstuck and cause a leak.
Windscreen could be leaking .
Very rare but the bulkhead has sealent in places , if this has perished then it could cause a leak .. not come accross this before but have herd of it once .
A/C drain is in that place but if the car is not running then it cant be that .
I assume you poured water into the sunroof and it came out the wheel arch liner and looked like the same amount ? if so then thats ok .
Ok so if i had the car in and wasn,t sure i would remove the panel under the glove box , maybe even remove the glove box , i would pull up the carpet that side so i could see where water would enter that area .. then someone with a hose on the car whilst i looked for where it was entering from .