Bleach characters have reishi bodies, a totally different form of matter from the regular matter(kishi) of the living world. It doesn't matter if they have bodily functions, it doesn't make them any less of a soul.
They are souls from the afterlife who still take part in reincarnation, They need to posses bodies to properly interact with the human world.
2. My point exactly. If he could phase things in him, he should have being able to phase through Madara's seal or even the Minato seals that were right on his skin. But he probably can't due to the mechanics of his phasing.
Yeah I know chakra is half spiritual energy. That doesn't give it the abilities of reiatsu,if that's what you are suggesting, same way reiryoku doesn't have the abilities of Chakra.