Currently, the 'Page Settings' dialog shows a warning below the 'Apply a new template' dropdown:
Components on the page might be repositioned if a new template is assigned.
This warning can be improved in two ways:
1. when the current page does not have any container items, the warning can be omitted
2. when the current page does have container items, and the newly selected template/prototype does not have any containers, all containers items will be removed. That should be stated in a more prominent (i.e. RED) warning box. Example message: "The selected template does not have any containers. All container items on the current page will be deleted if this template is applied."