In custom_theme/admin_custom_theme_config.php you can submit a part of the URI to identify pages where you want a custom theme to be rendered, just like you do in e107_admin/menus.php?configure to select pages where a menu is to be shown or hidden.
If you want to display a specific theme with a specific news article, let's say news.php?extend.10 and similarly news.php?item.10, the first of the two has its URI rewritten, where extend.10 becomes extend_10 (the period, or dot, is replaced with an underscore). This is not the case as long as you only want to render a custom theme with only one of the two types of news.php URI's (item or extend), but always the case when you tell custom_theme to render a specific theme with both URI's (in two separate boxes).
How come ?
Wouldn't it also be great if the e107_admin/menus.php?configure style text area was to be used in the same manner with custom_theme as well? It is so much easier to have all the pages listed on top of each other in a single text area than to select a theme from a drop down list for each page, as you have to do now.