Update documentation for model changes

We have made various changes to the behaviour of the model and are planning more. Once we've finished the main model changes for this engagement, we should have another pass at the documentation to update it. It probably doesn't make sense to make big changes as we go along as the model might well be changed again before the next release anyway.

Relevant issues:

- [ ] #1199
- [x] #1201
- [ ] #1347
- [x] #1358

Relevant PRs:

- [ ] #1365
- [ ] #1349

Please comment below if you change something else that needs documenting, so we have a to-do list.