$products = $this->productFactory->create()
     ->getCollection()
     ->addStoreFilter(2)
     ->addAttributeToFilter('custom_attribute', '123');

SELECT `e`.*, IF(at_custom_attribute.value_id > 0, at_custom_attribute.value, at_custom_attribute_default.value) AS `custom_attribute`
FROM `catalog_product_entity` AS `e`
INNER JOIN `catalog_product_website` AS `product_website` ON product_website.product_id = e.entity_id AND product_website.website_id = 2
INNER JOIN `catalog_product_entity_varchar` AS `at_custom_attribute_default` ON (`at_custom_attribute_default`.`entity_id` = `e`.`entity_id`) AND (`at_custom_attribute_default`.`attribute_id` = '163') AND `at_custom_attribute_default`.`store_id` = 0
LEFT JOIN `catalog_product_entity_varchar` AS `at_custom_attribute` ON (`at_custom_attribute`.`entity_id` = `e`.`entity_id`) AND (`at_custom_attribute`.`attribute_id` = '163') AND (`at_custom_attribute`.`store_id` = 2) WHERE (IF(at_custom_attribute.value_id > 0, at_custom_attribute.value, at_custom_attribute_default.value) = '63801')