Scenarios that disable ini_set fail since 5.4.0 #416

Since 5.4.0, scenarios that run WP-CLI with ini_set disabled (-ddisable_functions=ini_set) fail with:

Call to undefined function WP_CLI\ini_set() in php/WP_CLI/Runner.php:3112

This breaks the WP-CLI framework tests on main (example run) and blocks wp-cli/wp-cli#6444 and wp-cli/wp-cli#6445. The likely trigger is the PHP settings added in #401.

Part of #394.