Consciousness does seem to be the ghost in the machine, or maybe, as it sometimes seems, the machine is the ghost in consciousness.
All we can do to try to peel away a few of the layers and see what happens, then try again.
As for transcendence, that's simple enough. We, as consciousness, are the energy always trying to transcend the forms we find ourselves in, creating ever more elaborate forms and trying to transcend those. It's like consciousness is always just one step beyond the thought or perception it currently is having. Sometimes the next trick is trying a little schizophrenia. Trying to be both the observer and the observed. What you will find is a fuzzy state, rather than two distinct entities. Like in a relationship, where you are not sure where you end and the other begins. The waves undulating, rather than the squiggly line we model them as.
As for the physics, it's bit of a Catch 22. Obviously they are seriously going off the rails, with multiverses and multiworlds, etc. As I see it, the real problems go much conceptually deeper than this generation of theorists can wrap their minds around. It is a classic situation of only those following the program can advance, so the basic premises cannot be questioned. What will happen eventually will be a reaction, rather than a continuation, as some generation comes along, that refuses to devote their lives to untestable theories. I used to think it's still a few decades into the future, having watched this generation grow old, chasing after ideas already shaky. Yet given the rapidity of the current cultural implosion, I suspect it will carry over into other areas that are currently going by past successes, than any future direction.
It's like being the cat and wondering when and if the glass vial is going to break. It is and isn’t. Fuzzy.