No, the scans say that he had "no sense of self beside his own consciousness", it means that everything else that makes his existence, beside his consciousness, weren't there anymore. Which, I mean, is logical, he was in a "dream-like" state.
Not really.
What I mean is that, obviously, if I kill you in body, mind and whatever your existence is made off, obviously your sense of self will crumble away. That's not my doing, however, it's merely how a concept linked to the physical/metaphysical component of reality should work. I think that's what CM type 3 is for? idk. Basically, if nothing remains, you can't have a "sense of self" anymore, since you're not there anymore.
What Yogiri is doing is not "destroying the parts to kill the origin" it's "destroying the origin while letting the parts alone". Exceptions exist, of course, like when he kills the arm of someone, he obviously doesn't kill the sense of self of the person, but merely the "existence" of that arm.