hi im unsure if it will be possible to repair, but my superb had water ingress issue quite some time ago when my dad had it but now i have it i wish to resolve the issues my dad left with the car.

Firstly the key fob is useless. it does nothing what so ever.. I have replaced the battery and it still has no effect on the car. So to unlock the car i use the key in the drivers door (which for some reason only unlocks drivers door) then i have a short wait to get the key in the ignition and turn the ignition or else the alarm sounds.

Is it possible to reprogram it to work? or is the entire central locking/ alarm lost and non repairable.

Additionally, is it possible to get the car programed to have the puddle lights (under the doors) come on when the interior lights are one? (such as the door opens and all interior lights come on including the puddle lights, or when the interior light is on manually)

I would guess the CECM is dead (under the passenger seat & carpet).

Replace that along with any corroded nodes and you have half a chance of getting some of the bits working again.

sounds like the water ingress has got to the wiring on the floor the first thing that I would do is remove the passenger seat and take a look at the joints in the wires particularly the ones behind the seat (look up water ingress cure on the forum) If you do have a problem here it effects the puddle lights, interior lights, windows, to name but a few. A tip for you the best way to rejoin these wires is get a small gas soldering iron and some shrink tube this works a treat unlike what the VW boys done going to the local toy shop and buying their connections there.