Constructor in a custom entity isn't prior to baseFieldDefinitions
Entity::create gets the storage for the entity type and calls  EntityStorage::create. What you are looking for is probably the method 
Entity::preCreate, which is the first entity event invoked by EntityStorage::create.

Place it as public static function in the custom entity class to change the values before the entity is created:

class CustomEntity extends ContentEntityBase {

   /**
   * {@inheritdoc}
   */
  public static function preCreate(EntityStorageInterface $storage, array &amp;$values) {
    // modify $values
  }

}