Document mutation mode and change site mode description

[gregorgorjanc]

Mutation mode is described in https://github.com/tskit-dev/tskit/issues/3299 and related work is in https://github.com/tskit-dev/tskit/pull/3266 and https://github.com/tskit-dev/tskit/pull/3271.

The current docs say site: How many mutations differentiate these two genomes? https://github.com/tskit-dev/tskit/blob/e4ca46969bb32f3de612c5653ba280446f4b9f5e/docs/stats.md?plain=1#L212. This should be something like `site: How many alleles differentiate these two genomes?.

Similarly at https://github.com/tskit-dev/tskit/blob/e4ca46969bb32f3de612c5653ba280446f4b9f5e/docs/stats.md?plain=1#L224

Best to search for all site hits in the stats.md file (possibly elsewhere).