Using a child theme, you can upgrade "gracefully". When you create a template file in your child theme, the template in the parent is ignored.
Toolbox is meant as a manual template for making your own parent theme, which will only be updated by you. As long as you don't let any user submit data (a create forms, handle POST data) to be displayed or to update WordPress as files or to save into the database, you are pretty safe. The "template tags" (WordPress functions for theme templates) just receive (read) data from WordPress. Those data are "sanitized" and safe to display.
Your theme might change the behaviour of WordPress through hooks (actions and filters). Let those actions fire without using anything that comes from a client (browser, user), and you are safe.