VCF only contains variant information; FASTQ and BAM contain the “raw” sequencing information (in reality that data is already heavily processed but it’s the starting point for all usual analysis). Depending on how you do the analysis, the variant data will be slightly different. There are some current baselines (so-called “best practice” workflows) for performing the analysis but many of the details are variable, and subject to much current research.

To be fair, for most things the VCF is completely sufficient (and in fact most people won’t care even about that). It just feels cooler to be in control of the raw data (and personally if I end up using a sequencing service, I would want to perform my analysis; but this is obviously irrelevant for 99.99% of users).