Hi Niels,
CLIENT SIDE
Since PHP code is executed on the server, it is not possible to inject code from a browser.
SERVER SIDE
The Code Manager saves your PHP code in the database. From there, PHP code execution follows the same rules as PHP code execution from a PHP file. Access to a PHP file is needed to inject code. This is the same with the Code Manager. Access to the database is needed to inject code.
NETWORK
Use HTTPS.
The plugin allows only admin users to save PHP code in the database. It checks the admins login and adds an additional token to validate the admins action. This is the standard way to secure WordPress dashboard actions. It would of course be possible to change saved code using a tool like MyPhpAdmin. Like admin users, I presume MyPhpAdmin users are trusted users.
To inject code into a PHP file, ftp or WordPress dashboard access is needed. To inject code into the database, WordPress dashboard or database access is needed. For both options you need to keep your accounts safe.
Does this answer your question?
Best regards,
Peter