Tried on fresh 8.4.x and also 8.3.5, to reproduce:
1. Enable 'Field Layout' module.
2. Edit some 'Content type', under 'Manage display' change 'Layout settings' to 'Two column', save.
3. Change formatter or its settings and save changes.
4. Try moving field to another region, observe the formatter/settings getting reset to defaults.
Also checked widgets under 'Manage form display' but they seem to work fine.