It doesn't matter if the car was stripped of all paint and fully resprayed any colour then built using all genuin S1 parts.
The fact is that the shell is NOT an original S1 she, and therefore it is NOT an S1.
If it has an S1 chassis number and reg - where did it come from and how did it get on the car? It must have been added to the shell and replaced the original chassis numbers, therefore it is a ringer.
The problem is that the shell is from an earlier car, before the S1 was created so it can't be factory.
If the correct shell had been used, then this would never have came to light, as many S1's have been rebuild and have new floor pans etc. Maybe when the car was rebuilt, whoever built the car put new floor pans in and applied to have new numbers stamped in, but decided to use the donor S1 ID rather than the ID of the shell?