WordPress plugin proof of concept for disabling the Stop Emails plugin from logging emails when run from the command line. See https://github.com/salcode/stop-emails/issues/15

wp-cli-test-stop-emails.php

<?php
/**
 * Plugin Name:     WP CLI Test Stop Emails
 * Plugin URI:      https://github.com/salcode/stop-emails/issues/15
 * Description:     Test plugin for <a href="https://github.com/salcode/stop-emails/issues/15">Issue 15</a>
 * Author:          Sal Ferrarello
 * Author URI:      https://salferrarello.com/
 * Text Domain:     wp-cli-test-stop-emails
 * Domain Path:     /languages
 * Version:         0.1.0
 *
 * @package         Wp_Cli_Test_Stop_Emails
 */

if ( ! class_exists( "WP_CLI" ) ) {
	return;
}

WP_CLI::add_command( 'test-email', function() {
	wp_mail(
		'to@example.com',
		'My Test Email',
		'This is a test email that should be caught by the Stop Emails plugin',
		[
			'From' => 'from@example.com',
		]
	);
} );

add_filter( 'option_fe_stop_emails_options', function( $fe_stop_emails_options ) {
	if ( isset( $fe_stop_emails_options['log-email'] ) && 1 === $fe_stop_emails_options['log-email'] ) {
		WP_CLI::log( 'My Plugin is suspending the Stop Emails Plugin from Logging Emails when run from WP CLI' );
		$fe_stop_emails_options['log-email'] = 0;
	}
	return $fe_stop_emails_options;
} );