Which databases does `mysqlpump` ignore by default?
The easiest way to know is to test, on Percona Server for MySQL 5.7.28 (latest as of this writing) it shows that mysqlpump includes the mysql schema in the backup:

CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mysql` /*!40100 DEFAULT CHARACTER SET latin1 */;
CREATE DATABASE /*!32312 IF NOT EXISTS*/ `mytest` /*!40100 DEFAULT CHARACTER SET latin1 */;
CREATE DATABASE /*!32312 IF NOT EXISTS*/ `test` /*!40100 DEFAULT CHARACTER SET latin1 */;