TBH I am not dure where this OP belongs, so Mods, please move if you think of a better place.

My Fabia is just out of warranty and naurally, whilst the warranty was in force, I has the servicing done by the local main dealer. The 3 year service cost

In practice it will make virtually no difference on a 4 or 5 year old car if the last couple of services were done at a competent independent garage rather than a main dealer.

If you part-ex it you will just be asked if it has a service history , and if you sell it privately the buyer will be happy as long as the book has been stamped at the right time and you have the invoice from the garage to back it up.

It's very rare for anyone to need to claim on the bodywork warranty

There is no requirement in the Body Warranty for my 2002 Octavia for the car to be inspected at regular intervals.

i'm not sure how it work with skoda but i had a mondeo and had the services done at a non ford service centre they did the service as per ford which included the paint and body work this was recorded in the service book and didn't void any part of the warrenty

As Denis said, I don't believe there is any requirement at service time for the body and paint work to be inspected.... I think as long as the garage can prove they followed Skoda's service procedures then you'll have no issues....

Chris