Who cares if the brain stem is fully functional at the time of NDE? I'm no neuroscientist, but the last I heard that part of the brain controls autonomic functions and shit.
I think consciousness is supposed to reside somewhere in the neocortex/frontal area. When we're having an experience, corresponding associations are registered on EEGs, so obviously as far as neuroscience is concerned a flat EEG equals loss of consciousness and no experience. Is this in dispute?