`SET PERSIST ONLY innodb_sys_tablespace_encrypt`="ON" created an entry in the mysqld-auto.cnf and would cause a server restart to fail.

It is noticed while testing PS-3822, introduces a new bootstrap variable:
1. innodb_sys_tablespace_encrypt

This variable must be passed while initialising the data directory. If the data-dir is not initialised with this option, the default is OFF and if attempted to start the server with
--innodb_sys_tablespace_encrypt=ON will return an error

However, it is noticed that
SET PERSIST_ONLY innodb_sys_tablespace_encrypt = ON;

executed successfully without any error which is incorrect behaviour
secondly, it creates an entry in mysqld-auto.cnf due to which during next  restart, the server refuses to come up

mysql> set persist_only innodb_sys_tablespace_encrypt = ON;
Query OK, 0 rows affected (0.01 sec)

mysql> show global variables like 'innodb_sys_tablespace_encrypt';
------------------------------------+

------------------------------------+

------------------------------------+
1 row in set (0.01 sec)

2019-05-24T06:26:52.194734Z 1 [ERROR] [MY-011825] [InnoDB] The system tablespace is not encrypted but --innodb_sys_tablespace_encrypt is ON. This instance was not bootstrapped with --innodb_sys_tablespace_encrypt=ON. Disable this option and start server