SELECT 
  storefronts.* 
FROM 
  cscart_storefronts AS storefronts 
  LEFT JOIN cscart_storefronts_companies AS companies ON storefronts.storefront_id = companies.storefront_id 
WHERE 
  1 = 1 
  AND (
    companies.company_id IN ('2')
  ) 
GROUP BY 
  storefronts.storefront_id 
ORDER BY 
  storefronts.is_default desc

Query time 0.00033

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "storefronts.is_default desc",
      "temporary_table": {
        "table": {
          "table_name": "companies",
          "access_type": "index",
          "possible_keys": ["PRIMARY", "idx_storefront_id"],
          "key": "PRIMARY",
          "key_length": "8",
          "used_key_parts": ["storefront_id", "company_id"],
          "rows": 3,
          "filtered": 100,
          "attached_condition": "companies.company_id = '2'",
          "using_index": true
        },
        "table": {
          "table_name": "storefronts",
          "access_type": "eq_ref",
          "possible_keys": ["PRIMARY"],
          "key": "PRIMARY",
          "key_length": "4",
          "used_key_parts": ["storefront_id"],
          "ref": ["cscart_purchase_fl_com.companies.storefront_id"],
          "rows": 1,
          "filtered": 100,
          "index_condition": "storefronts.storefront_id = companies.storefront_id"
        }
      }
    }
  }
}