SELECT 
  c.*, 
  IF (c.location_id != 47, 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') 
  AND c.company_id = 0

Query time 0.00534

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "c",
          "access_type": "ALL",
          "possible_keys": [
            "location_id",
            "location_id_company_id",
            "location_id_position_company_id"
          ],
          "rows": 316,
          "filtered": 100,
          "attached_condition": "c.company_id = 0 and c.position in ('TOP_PANEL','HEADER','FOOTER')"
        }
      },
      {
        "table": {
          "table_name": "l",
          "access_type": "eq_ref",
          "possible_keys": ["PRIMARY"],
          "key": "PRIMARY",
          "key_length": "3",
          "used_key_parts": ["location_id"],
          "ref": ["dev_db.c.location_id"],
          "rows": 1,
          "filtered": 100,
          "attached_condition": "l.is_default = 1 and l.layout_id = 3"
        }
      }
    ]
  }
}