Is the Filter Theory committing the ad hoc fallacy and is it unfalsifiable?

Yes. 

The biggest limitation of this aircraft electronic system analogy seems to be that with the human mind/brain but not with the pilot/interfacing aircraft electronics system, the interface with the vastly complex mechanisms of the brain is totally unconscious, and to the conscious mind the interface is totally transparent with the human coming to identify him/her self with the system as a whole.

I do like the dashboard of the craft proposed, it matches with Essentia Foundations argument that evolution adapts us to see very little of reality:




I think the challenge is how to incorporate things like brain-based illnesses. This is where I think the division between user and "avatar" in a VR environment helps to some degree, as there is in-game memory that will affect how the character can proceed.

There really isn't anything quite like the brain-mind relationship though so all analogies will fall short in some way.