It doesnt work with relationship.

As example

a view of nodes with relationship to commerce products (display->products)

The product entity, contains an taxonomy field.

the query looks like

SELECT node.created AS node_created, node.nid AS nid
FROM
{node} node
LEFT JOIN {field_data_field_product} field_data_field_product ON node.nid = field_data_field_product.entity_id AND (field_data_field_product.entity_type = 'node' AND field_data_field_product.deleted = '0')
LEFT JOIN {commerce_product} commerce_product_field_data_field_product ON field_data_field_product.field_product_product_id = commerce_product_field_data_field_product.product_id
WHERE (( (node.status = '1') AND (node.type IN ('product_display')) AND (node.nid IN (SELECT tn.nid AS nid
FROM
{taxonomy_index} tn
WHERE ( (tn.tid = '507') ))) ))
ORDER BY node_created DESC
LIMIT 10 OFFSET 0

but it's wrong. taxonomy_index is attached to nodes, not to entities. So, it doesnt work with relationship.

Sorry for my english.