SELECT 
  c.*, 
  IF (c.location_id != 99, 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 = 6 
WHERE 
  1 
  AND c.position IN ('TOP_PANEL', 'HEADER', 'FOOTER')

Query time 0.00151

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "39.81"
    },
    "nested_loop": [
      {
        "table": {
          "table_name": "l",
          "access_type": "ALL",
          "possible_keys": [
            "PRIMARY"
          ],
          "rows_examined_per_scan": 339,
          "rows_produced_per_join": 3,
          "filtered": "1.00",
          "cost_info": {
            "read_cost": "34.73",
            "eval_cost": "0.34",
            "prefix_cost": "35.07",
            "data_read_per_join": "3K"
          },
          "used_columns": [
            "location_id",
            "is_default",
            "layout_id"
          ],
          "attached_condition": "((`test_uchur_k`.`l`.`layout_id` = 6) and (`test_uchur_k`.`l`.`is_default` = 1))"
        }
      },
      {
        "table": {
          "table_name": "c",
          "access_type": "ref",
          "possible_keys": [
            "location_id",
            "location_id_company_id",
            "location_id_position_company_id"
          ],
          "key": "location_id",
          "used_key_parts": [
            "location_id"
          ],
          "key_length": "3",
          "ref": [
            "test_uchur_k.l.location_id"
          ],
          "rows_examined_per_scan": 4,
          "rows_produced_per_join": 6,
          "filtered": "50.00",
          "cost_info": {
            "read_cost": "3.39",
            "eval_cost": "0.68",
            "prefix_cost": "39.81",
            "data_read_per_join": "2K"
          },
          "used_columns": [
            "container_id",
            "location_id",
            "position",
            "width",
            "user_class",
            "linked_to_default",
            "status",
            "company_id"
          ],
          "attached_condition": "(`test_uchur_k`.`c`.`position` in ('TOP_PANEL','HEADER','FOOTER'))"
        }
      }
    ]
  }
}