I always make megedarra with brown rice, though I use the stove top (for my own recipe, which is on this site, and which uses shallots as well). The issue is with the cooking time, since brown rice takes up to 50 minutes to cook, and the combined cook time here is 35 minutes. Maybe if you put in the rice first and gave it a head start (and additional boiling water), but it might require a bit of experimentation!
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I'm really curious how the shallots remain crispy after all that time in a sealed pan with quite a bit of water . . . . . ;o)