Used to think hidden fasteners were just for looks... but that epoxy fill trick sounds like it actually locks everything down tight. Might have to try that on my next build.
Yeah, that bit about the epoxy making the wood split is what worries me too. I love the clean look, but wood moves so much with the seasons. If that epoxy plug is totally rigid, something's gotta give. It seems like it could put a ton of stress right around the bolt head over a few years. Maybe a more flexible filler would be a safer bet for the long haul.