I'm guessing this means we'll still be able to plug the rudder through the Cougar to a USB port and pick up the Rudder and assign as an axis in A:10C? As far as I can tell, there is not Rudder port to USB convertor that will work without the Cougar.
Currently, not without scripting, no, you won't.
When you build a T.A.R.G.E.T. profile, you tell T.A.R.G.E.T. which physical axes get assigned to DirectX axes. the rest of the physical axes don't get assigned to any
DirectX axis. So, in effect, if you don't assign your Cougar rudder axis to a DirectX axis in T.A.R.G.E.T., then when you run the T.A.R.G.E.T. profile there will be no Cougar DirectX axis. The problem right now is that T.A.R.G.E.T. won't let you assign the Cougar rudder axis at all. This is a bug, and Thrustmaster is working to fix it. What T.A.R.G.E.T. needs is the ability to "ignore" to Cougar entirely, and right now it doesn't do this.
One way to work around this would be to unplug your Cougar, start T.A.R.G.E.T., run the profile, and then plug in the Cougar.