SELECT 
  user_id 
FROM 
  cscart_users 
WHERE 
  company_id = 20 
  AND user_type = 'V' 
  AND status = 'A' 
ORDER BY 
  is_root DESC, 
  user_id ASC 
LIMIT 
  1

Query time 0.00054

JSON explain

{
  "query_block": {
    "select_id": 1,
    "read_sorted_file": {
      "filesort": {
        "sort_key": "cscart_users.is_root desc, cscart_users.user_id",
        "table": {
          "table_name": "cscart_users",
          "access_type": "ALL",
          "rows": 96,
          "filtered": 100,
          "attached_condition": "cscart_users.company_id = 20 and cscart_users.user_type = 'V' and cscart_users.`status` = 'A'"
        }
      }
    }
  }
}