Update discussion of atom mapping from original best practices

[fjclark]

Proposed Change

Update the atom mapping discussion moved here from the first paper (alchemistry/alchemical-best-practices#145).

Proposed Authors and Reviewers

Please volunteer (before the end of January) to author/ review and state when you're available. Authors, please say roughly when you plan to contribute the changes (no later than the end of May).

Proposed author: @RiesBen?
Proposed reviewer: Volunteer wanted