If you disassemble what you have, you'll see a length of sleeve with a rib on it that goes from the top headset bearing's wedge ring to just above the top of the steerer where the preload cap does its job, independent of your oddball stem clamped to the sleeve.

Now, with just the bare steerer poking out of the bearing, put your bag-holding stem on like normal because it's a normal stem, and then put the sleeve on. The sleeve is now the normal stem's stack height too long, see? Cut that much off the sleeve, put it back on along with the oddball stem holding your bars above the normal stem holding your bag, and the top cap will bear down on the headset via the sleeve and normal stem. Clamp the stems after setting bearing preload, viola.