[PP-1] Entity API bug affecting REST: "last changed" timestamp not updated and "create new revision" setting not respected when PATCHing via REST

Problem/Motivation

1. the "last changed" timestamp is not updated when updating entities via REST
2. the "create new revision" setting on node types is not respected when updating entities via REST

Proposed resolution

Fix this, and add test coverage.

Remaining tasks

1. Fix the underlying root cause, in 🐛 Move entity preparation from form controller to entity class: "last changed" timestamp not updated and "create new revision" setting not respected when updating entities via Entity API Postponed: needs info
2. Add test coverage in this issue

User interface changes

None.

API changes

None.

Data model changes

None.