Daniel, with such an erudite response I would have thought you'd have checked my diagrams...
The sectional drawings are identical in dimension and the point of rotation is the one about which the engine was rotated - the crankshaft centreline.
Run a ruler across the drawing as they are put together (with the crank centreline as the datum point) and you'll see that there is a part of the head in the slant that rises above the top of the head in the vertical drawing.
My purpose in all of this was to show what is absolutely true... that the height of the engine, the effective height, the highest point as it would affect the fitment under the hood, is the air cleaner and that the air cleaner would not typically be any higher if the engine were vertical. The manifold runs at the same height in both as the ports are at the same height, so with the same design ideals the carburettor and air cleaner would be at the same height.
I don't want to completely trounce your suggestions, but just one other thing. There are, as I posted previously, plenty of vertical inline engines with the water pump offset. Moving the fan a couple of inches to one side should not be a big deal and it isn't in the Nissan engine I cited as an example.
Now to explain, I am not here to beat my own drum, to convince people I'm an expert or anything like that. But when I see that there is a mistaken belief abroad I like to explain why it isn't so. I would have blindly accepted the 'lower engine height' story had I not worked this out years ago with the Peugeot engines that are canted at 45°. With those engines the camshaft is on the 'high' side of the engine and therefore the intake side of the head stands out even further, hence the intake manifold is thrust right up there by the canting of the engine.