Bob chose to be rational and concede when presented with a proper argument, instead of choosing to be an asshole.
Being rational doesn't entail (publically) conceding to proper arguments or not being an asshole.
It does in many (probably most) practical contexts.
Would it be supercilious to thank someone for updating? I know I would feel uncomfortable doing it, but I often feel the urge to do so anyway.
There seems to be something vicious about thanking them. My own estimation of my own belief has not changed in these situations. I feel fairly satisfied that the other has considered my view and has shakily come to agree with it. I worry it would be a little like saying 'screw your opinion, now you see I'm right.'
However:
It is both rational and polite to thank them. The gentlemen's agreement of rationality allows for one person to be wrong and not lose face at all. When someone concedes something to me (a point) I typically feel the need to thank them.
What do you think?