Thanks for the suggestions.
I'm pretty sure the creaking noise is coming more from the centre of the dashboard, i.e. the glove box area, which according to the owner's manual is where the air filters kept. Actually they've also given instructions on how to take out and inspect the filter (P225/226). Think I may give it a go to see whether there's any obvious location for the noise.
I'll definitely give that silicon spray a go over the driver's door seal.
I suppose if any of the noises remain I could always take it back to the dealer again to see what they can come up with, luckily its all done under warranty.