Bookmark apps not created by explicitly by dragging a link into the chrome://apps page should not appear in chrome://apps (or the Chrome OS app launcher.)

1. That an icons on the desktop corresponds to an "app" created behind the scenes by Chrome is an implementation detail. A user may understandably be confused when a website suddenly appears in the Apps list. Creating a desktop icon is akin to adding a page to the Bookmarks bar, which doesn't add it to chrome://apps.

2. If a bookmark app points to an extension (e.g., open an extension page like Secure Shell, then add to desktop), removing that bookmark app from chrome://apps could mislead you into thinking you've removed the actual extension the bookmark app pointed to. (The 'Confirm Removal: Remove "
<extension name>"?' dialog itself is ambiguous.)