I think the idea, at least for Windows, is that extensions are a legacy thing, and are still supported because they are the basis for determining file type. BUT, the reasoning is likely that they can be hidden from the user and only show the user the actual file type. Which is fine in theory, except that now you are training the user to recognize file type solely by icon, making it trivial to give a dynamic-icon type (like EXE, or the old SCR which users are unlikely to recognize) the same icon as a text file and subvert the user's expectations and make them think the file is safe. If you are not in Details mode or not grouping by File Type it is IMPOSSIBLE to reliably determine the type of a file without the extension!
Of course MS has added the whole Zone Identifier scheme and displays a nasty warning when trying to run dangerous files from the internet. I think this is a good measure to prevent this type of trickery, unfortunately people tend to click past such dialogs.