My MK4 anni had the wings done due to corrosion and they explained that it was the sponge in the wing that retains water and causes the rust to start. This is similar to the mk5, the sponge is there i believe to stop the arch liner vibrating.
When looking for my ed30, i saw many 07,57, even an 08 plate with arch and sill rot, some very badly repaired. The 08 plate one had large sections of paint flaking off and only 28k on the clock, according to the main dealer, JCT600 it was to be expected due to the age!