The last sequence plays more like an impressionist sequence; Hedwig runs off and either re-emerges as Tommy or disappears and the actor playing Hedwig doubles as Tommy. It's not clear to me that the show, as written and produced, makes its intention obvious. It deliberately blurs that line, and so one is asked to reckon what to make of that sequence. Is it a mental breakdown for Hedwig/Tommy where trauma is exorcised onstage? Is the convention of Hedwig's one-night-only concert dismantled and we in the audience are transported to Tommy's cocnert outside? Has Hedwig left our theatre and Tommy entered, in a daze of self-discovery?
There are many possible interpretations to me, and while the most logical ones involve Tommy and Hedwig being distinct individuals, I can see how one could interpret it otherwise, as written and produced.
Words don't deserve that kind of malarkey. They're innocent, neutral, precise, standing for this, describing that, meaning the other, so if you look after them you can build bridges across incomprehension and chaos. But when they get their corners knocked off, they're no good anymore…I don't think writers are sacred, but words are. They deserve respect. If you get the right ones in the right order, you can nudge the world a little.