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 ('12')
  ) 
GROUP BY 
  storefronts.storefront_id 
ORDER BY 
  storefronts.is_default desc

Query time 0.00020

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "2.56"
    },
    "ordering_operation": {
      "using_filesort": true,
      "grouping_operation": {
        "using_temporary_table": true,
        "using_filesort": false,
        "nested_loop": [
          {
            "table": {
              "table_name": "companies",
              "access_type": "index",
              "possible_keys": [
                "PRIMARY",
                "idx_storefront_id"
              ],
              "key": "idx_storefront_id",
              "used_key_parts": [
                "storefront_id"
              ],
              "key_length": "4",
              "rows_examined_per_scan": 11,
              "rows_produced_per_join": 1,
              "filtered": "10.00",
              "using_index": true,
              "cost_info": {
                "read_cost": "1.24",
                "eval_cost": "0.11",
                "prefix_cost": "1.35",
                "data_read_per_join": "17"
              },
              "used_columns": [
                "storefront_id",
                "company_id"
              ],
              "attached_condition": "((`biobronz_storeh`.`companies`.`company_id` = 12) and (`biobronz_storeh`.`companies`.`storefront_id` is not null))"
            }
          },
          {
            "table": {
              "table_name": "storefronts",
              "access_type": "eq_ref",
              "possible_keys": [
                "PRIMARY"
              ],
              "key": "PRIMARY",
              "used_key_parts": [
                "storefront_id"
              ],
              "key_length": "4",
              "ref": [
                "biobronz_storeh.companies.storefront_id"
              ],
              "rows_examined_per_scan": 1,
              "rows_produced_per_join": 1,
              "filtered": "100.00",
              "cost_info": {
                "read_cost": "1.10",
                "eval_cost": "0.11",
                "prefix_cost": "2.56",
                "data_read_per_join": "2K"
              },
              "used_columns": [
                "storefront_id",
                "url",
                "redirect_customer",
                "is_default",
                "status",
                "access_key",
                "name",
                "theme_name",
                "is_accessible_for_authorized_customers_only"
              ]
            }
          }
        ]
      }
    }
  }
}