You use all of the parts just as you would with an open closure.
That certainly wouldn't be possible with the closure I have, which I think is what the OP is asking about also (and Justin mentioned above). As mentioned, the closure has a metal lip at the front that is the size of the "Delay O-Ring" as it's named in the CRDK instructions. So this means two things:
1) The 'Forward Delay Spacer (13/16" O.D. Washer)' wouldn't lay flat, since it's the diameter of the entire cavity, and that diameter isn't maintained to the bottom of this closure's cavity.
2) The 'Delay O-Ring' would sit on top of this lip rather than going all the way to the front of the delay cavity
So if these two pieces are installed, you end up with a big air-pocket at the front of the closure, and the delay itself will not seat fully into the delay cavity (it sticks out by the thickness of the two above-mentioned parts) and could interfere with the motor grains. Or if you leave these two pieces out everything fits exactly as it does in other 38mm forward closures, flush with the surface of the closure.
So I'm not sure that all of the 38mm plugged/threaded forward closures have this, but there are definitely some that do (I only have one, so it's 1 out of 1 for me).
My closure is already fully-assembled / waiting to fly from a flight I didn't get to do at LDRS this year, so I can't take a picture of the empty cavity right now.