I don't think so, although I don't have any hard references to back this up.
The file system check phases mostly deals with the system areas (FAT, MFT, etc) and not with the data portion itself, which is what is "defragmentation" deals with. It just checks that the files can be retrieved in full, that all pointer references are correct and similar validations, that are not affected by fragmentation.
As for the surface analysis phase, it reads every data sector in the disk, regardless if its occupied or not, without caring about its contents. Once again, fragmentation doesn't matters here.