Improve update_all when FROM is a subquery

After working in
https://gitlab.com/gitlab-org/gitlab/-/merge_requests/46260, we have
learned that the UPDATE statement was incorrect because the SQL code
doesn't include the subquery.

This change partially reverts the changes in c2b330dc.

This is not a bug because:
- If a project has an issue tracker integration or an external wiki
  integration, `has_external_issue_tracker`/`has_external_wiki` is
  already `true`, so we just were updating it again with `true`. This
  commit avoids this scenario.
- If a project doesn't have an issue tracker integration or an external
  wiki integration, `has_external_issue_tracker`/`has_external_wiki` is
  `false`, so we update it to `true`.

app/services/bulk_create_integration_service.rb

@@ -33,15 +33,17 @@ class BulkCreateIntegrationService
     klass.insert_all(items_to_insert, returning: [:id])
   end
 
+  # rubocop: disable CodeReuse/ActiveRecord
   def run_callbacks(batch)
     if integration.external_issue_tracker?
-      batch.update_all(has_external_issue_tracker: true)
+      Project.where(id: batch.select(:id)).update_all(has_external_issue_tracker: true)
     end
 
     if integration.external_wiki?
-      batch.update_all(has_external_wiki: true)
+      Project.where(id: batch.select(:id)).update_all(has_external_wiki: true)
     end
   end
+  # rubocop: enable CodeReuse/ActiveRecord
 
   def service_hash
     if integration.template?