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Spin-off from. If a module implements hook_field_load() to add something that later functions (e.g., formatters) expect to be there (for example, in the case of datetime.module, it adds a $item['date'] object derived from the $item['value'] string), then EntityFormController::submit() overrides the field items with their new values, and destroys the stuff added by hook_field_load(), breaking those other functions unless the entity is saved and reloaded.
Not sure how to solve this yet. EntityNG supports a better way of implementing calculated fields, and that could be part of the answer.