Did Bakker ever get any lengthy consulting from anything like a neurologist, psychiatrist, systems theorist, or any sort of actual scientist to refine his Blind Brain Theory (theory incidentally meaning something very different within the philosophy of Science than in other philosophy; in the case of scientific philosophy I don't believe Blind Brain Theory actually qualifies as a theory) with actual peer reviewed, falsifiable data?
Otherwise, even if it makes perfect sense internally...there's no reason whatsoever to put any more faith in it than the ideas of thousands of other thinkers on the nature of human consciousness. Internal logic is not enough. The ancient Greeks had a perfectly internally consistent and mathematically elegant model for our universe. It was geocentric and composed of celestial spheres with intensely complex orbits and had no bearing on reality whatsoever.
A theory without verifiable predictions and without observational evidence is simply a guess. Scientifically, we call it a hypothesis. Which is a good start, but that's all it is.
I know he's very popular on this site, and he's a fantastic writer, and probably a good philosopher too (though I have no real philosophy training outside of science), but I'm really not sure he's qualified to talk about this issue at all.