Ive had i look at mine out of curiosity today, the engine bay i knew about so i looked at the spray gap when the doors open, i missed it at first but then i could see it from a certain angle. Im no car builder but i think the body is sprayed first then the panels and doors are fixed on and painted with the doors open then shut, so its seems that this is how the missed spray occurs. Ive got a seven year old mk5 also black and that is the same, i also looked at my 15 year old peugeot van which is red and at first it didn't look like it had it so then i wiped away the grime and it was there, not as noticeable but i think thats down to the colour and different door etc. So it wouldn't surprise me if alot of cars have this if you look for it.
mkivken my rear bumper were the number plate lights are seem fine, but im going to clean the car tommorow and have a good look.
The inner wheel wells, im not sure where you mean. Do you mean behind the plastic covers inside the wheel arches ?
The rust on mk5's id like to know where and ill check that aswell.