Auto-content filtering only affects files and thus has always worked with flat-view as far as I can tell. (We're talking about being able to use the drop-down to select *.xyz from the list of extensions in the folder, right?)
As for folder filters in flat-view, it's already back. See the 9.1.1.8 changelog for how to enable it if you want to use it.
Edit: Posted before I had seen Jon's nearly identical reply above. 