Below is a patch to FileDataObjectManager in the latest SVN of DOM to allow Uploadify fields to respect uploadFolder & allowed extensions. UC: is there an issue tracker / other workflow that's preferred for patch submissions?

Index: www/dataobject_manager/code/FileDataObjectManager.php
===================================================================
--- www/dataobject_manager/code/FileDataObjectManager.php   (revision 14)
+++ www/dataobject_manager/code/FileDataObjectManager.php   (working copy)
@@ -293,6 +293,16 @@
         }
      }
      
+      // [start] bb patch
+      if(!empty($this->allowedFileTypes))
+      {
+
+         $uploader->setFileTypes($this->getAllowedFileTypes(), $this->PluralTitle() . '(' . implode(',',$this->allowedFileTypes) . ')');
+      }
+
+      $uploader->uploadFolder = $this->uploadFolder;
+      // [end] bb patch
+      
      return $fields;
   }