The other thing you could do is get by without the PHP Execute plugin. IMO, the plugin is less than ideal anyway, it introduces some security vulnerabilities. Nothing exploitable by itself, but combined with other weaknesses, it could result in your site being compromised. The chance is small, but present.

One way to achieve PHP execution without the plugin (and improve security) is to develop your own shortcodes. Place the shortcode where you want PHP to execute. Make your PHP code into a shortcode handler.