Custom translatable content entity appears twice when choosing the entity type to create a view
I don't think it's directly associated with translation handling - it looks like it's the distinction between the entity and entity_field_data table. The "working" option in the dropdown is a class derived from WizardPluginBase.

I fixed my problem by making sure both of these were in my Drupal\custom_entity\Entity\CustomEntityViewsData::getViewsData 

$data['custom_entity']['table']['wizard_id'] = 'custom_entity';
$data['custom_entity_field_data']['table']['wizard_id'] = 'custom_entity';`