There has always been a clear distinction between what is considered rational thought and emotional behavior. The classical view is that rational thinking is more evolved than being emotional therefore the cortex, as a superb product of the evolution of brain must be responsible of the rational part of the self and the thalamic system, the one we share with birds and lizards must be the responsible of the emotions we feel.
Nobody doubts that the thalamic system’s reaction of run or fight don’t match many of modern’s life needs and that the difficulty to cope with one’s emotions can be a heavy nuisance. It is reason what has created science, tunnels that crosses the earth below seas and that has given birth to democracy. But we also see that the most superb forms of art are mixtures of reason and emotion in which it is difficult to say what is more important.
It wouldn’t be reasonable to say that during the thousands of millions of years before the apparition of a primary cortex brains where analyzing the world in a deficient way and reacting due just to blind impulses. Crocodiles and many birds art two kinds of very primitive creatures that have very well adapted brains able to recognize the world, distinguish colors and react in a very efficient non emotional way.
The primitive reptilian brain as the thalamic system is called is able to see in the animals that posses no cortex the same colors that we do and distinguish sounds as well as we do.
There is no need then to suppose that all what is rational comes from the cortex. Qualia is not restricted to animals with a cortex. If reptiles are able to distinguish colors and sounds then the qualia of those perceptions should be as primitive as the thalamic system. In evolution if something works well it is kept so qualia should arouse there.
The role of the cortex would be then to observe the world through reptilian eyes and to interpret in a more sophisticated way