I must point out reference genome is just that, and not a majority genome or anything like that. In other words, even if most people have brown eyes, there is no reason for reference genome to have brown eyes genotype: it just happens to do so in this case. But like any genome, reference genome also has rare variants, some of them probably even unique.
If people’s genomes are going to be encoded as diffs against the reference then it’d be most efficient of it were a majority genome to minimize average diff size.
Sure, but that’s not what Human Build 37 is. Maybe in the future.