Just to clarify, does "irreducible" in (3) also mean that qualia are therefore extra-physical?

Not unless we are arguing over definitions. Tabooing the phrase "extra-physical", what Eliezer and Chalmers were arguing (or trying to argue) about is whether a superintelligent observer, with full knowledge of the physical state of a brain, would have the same level of certainty about the qualia that the brain experiences as it does about the physical configuration of the brain.

Actually, if they had phrased the debate in those terms it would have turned out better. I don't think that what they were arguing about was clearly defined by either party, which is why it has been necessary (in my humble opinion) for me to "repair" Eliezer's contribution.

So anyway, no it does not mean the same thing. I argue that qualia are not "extra-physical", because the observer does in fact have the same level of knowledge about the qualia as it does about the physical Universe. However, this only proves that qualia supervene upon physical brain states and does not demonstrate that qualia can ever be explained in terms of quarks (rather than "psycho-physical bridging laws" or some such idea).

It might be tempting to refer to (a degree of) belief in irreducibility of qualia as "non-physical", but for the purposes of this discussion it would confound things.

So doesn't that leave us with two options:

1) Evolution went from single cell prokaryotes to Homo Sapiens and somewhere during this period the universe went "plop" and irreducible qualia started appearing in some moderately advanced species.

2) Qualia are real and reducible in terms of quarks like everything else in the brain. As evolution produced better brains at some point it created a brain with a minor sense of qualia. Time passed. Brains got better and more introspective. In other words: qualia evolved (or "emerged") like our sense of smell, our eyesight and so forth.

I don't think that there's a good reason why you didn't describe qualia as "plopping" into existence in scenario 2 as well, or else in neither scenario. Since (with extreme likelihood) qualia supervene upon brain states whether they are irreducible or reducible, the existence of suitable brain states (whatever that condition may be) seems likely to be a continuous rather than discrete quality. "Dimmer" qualia giving way to "brighter" qualia, as it were, as more complex lifeforms evolve.

Note the similarity to Eliezer's post on the many worlds hypothesis here.