Explore using conditionAggregate instead of conditions between all the joins

So D7 version does this to ensure that conditions are not matched to same endpoint multiple times.

   for ($i = 0; $i < $arity; $i++) {
     for ($k = $i + 1; $k < $arity; $k++) {
      $column_left = 'field_data_endpoints_delta_' . $i . '.endpoints_r_index';
      $column_right = 'field_data_endpoints_delta_' . $k . '.endpoints_r_index';
       $query->where("$column_left != $column_right");
     }
   }

Alternate way could be to use query aggregation and conditionAggregate if there are multiple references to same entity.