How? Science is based on making models from empirical observations about the world and yourself

Science requires falsafiability. It's fine to belive other things, but science it a method, not a belief system.

one of these empirical observations is the observation that your phenomenal consciousness actually exists, seemingly in opposition to the physical world, maybe we should perhaps include that fact in our models?

Nothing I've seen seems to imply it's outside of our models. You haven't explained why that's the case. We know how the humans brain and nervous system functions. It isn't magic anymore.