Review the Settings class and its defaults

[IAlibay]

The Settings class (https://github.com/OpenFreeEnergy/gufe/blob/main/gufe/settings/models.py#L212) is often used as "the class you should subclass when creating a Settings object for a Protocol".

However it has some preset fields that aren't appropriate for some Settings classes (for example the AHFE Protocol). This means that such Protocol Settings need to subclass SettingsBaseModel rather than Settings.

If we want a unified parent class for our Settings objects, we may need to review exactly what the Settings class contains.