SELECT 
  c.*, 
  IF (c.location_id != 40, 0, 1) as `default` 
FROM 
  cscart_bm_containers as c 
  INNER JOIN cscart_bm_locations as l ON c.location_id = l.location_id 
  AND l.is_default = 1 
  AND l.layout_id = 3 
WHERE 
  1 
  AND c.position IN ('TOP_PANEL', 'HEADER', 'FOOTER')

Query time 0.00105

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "29.42"
    },
    "nested_loop": [
      {
        "table": {
          "table_name": "l",
          "access_type": "ALL",
          "possible_keys": [
            "PRIMARY"
          ],
          "rows_examined_per_scan": 56,
          "rows_produced_per_join": 0,
          "filtered": "1.79",
          "cost_info": {
            "read_cost": "6.12",
            "eval_cost": "0.10",
            "prefix_cost": "6.22",
            "data_read_per_join": "231"
          },
          "used_columns": [
            "location_id",
            "is_default",
            "layout_id"
          ],
          "attached_condition": "((`maniamall_cscart`.`l`.`layout_id` = 3) and (`maniamall_cscart`.`l`.`is_default` = 1))"
        }
      },
      {
        "table": {
          "table_name": "c",
          "access_type": "ALL",
          "rows_examined_per_scan": 224,
          "rows_produced_per_join": 11,
          "filtered": "5.00",
          "using_join_buffer": "hash join",
          "cost_info": {
            "read_cost": "12.00",
            "eval_cost": "1.12",
            "prefix_cost": "29.42",
            "data_read_per_join": "4K"
          },
          "used_columns": [
            "container_id",
            "location_id",
            "position",
            "width",
            "user_class",
            "linked_to_default",
            "status"
          ],
          "attached_condition": "((`maniamall_cscart`.`c`.`location_id` = `maniamall_cscart`.`l`.`location_id`) and (`maniamall_cscart`.`c`.`position` in ('TOP_PANEL','HEADER','FOOTER')))"
        }
      }
    ]
  }
}

Result