The Factory Joint Rule
The factory joint MUST be installed in the floor. If it is not installed in the floor, the joint may give and your system will no longer work. Not only will your warrantee be voided but you will have to repair the joint and place it back into the floor.
To help with the height the joint adds, consider cutting a channel in the subfloor for the joint. This will help avoid adding height and maintain levelness in the floor.