No they did not have the car prior to her abduction. My question is how they know the DNA could not have come other sources, such as her little sister, who started wearing her clothes after she disappeared. Or Kate's clothes, which you would expect to have Madeleine's DNA all over them.
Presumably because they did not find the sister's or mother's DNA in the trunk but only Madeleine's - and a susbstantial amount at that.