I didn't read the five million words on the linked Valve developer page, so I'm not sure why you called it moot.

That video is a little outdated and... misleading. Now, all classes have the same hitbox size as a stationary heavy (up, down, left, right, front, and back) regardless of cl_lagcompensation or actual model size. Yes, the scout's 'spiritual(?) head' is about a foot higher than his actual head. Also, lag_compensation is enabled by default. So unless you messed with it, shooting the drawn model is the way to go. I think people with aimbots turn it off so they can kill people before they even appear on screen. That's kind of cool, I guess.

The main problems with hits are lag and discrepancies in weapon hitboxes, weapon speed, and places weapons hit. That's probably what your second link talks about. Don't know, though. All weapons firing bullets fire instantly while the visible tracer rounds take much, much longer. It's especially noticeable with miniguns. They start doing damage before the heavy has finished spinning up because of the delay between both players and the server.

On a side note, Valve must've been really drunk when they decided to legitimize side stabs in the same update they double the size of most classes' hit boxes.