Mrmnms - no, I believe what they're describing is:
A) Zeroing the angle cube on an empty blade table, where the knife would be, then placing the knife, setting the angle for proper sharpening (whatever that happens to be) and then measuring the angle of the rod with the stone resting on the blade edge.
B) Placing the knife on the blade table flat or pressed down in the sharpening position, then zeroing the angle cube on the knife itself, setting the angle for proper sharpening, and then measuring the angle of the rod with the stone resting on the blade edge.
The offset will essentially be the angle that the knife itself is introducing into the equation.
Rick and Madrookie's described shortcut method (which is great, by the way) is to:
1) Zero the cube on an empty EP, then place the knife in the sharpening position, placing the angle cube on the knife in the proper position that you tend to use when measuring, and seeing the difference in angle between the two.
2) Use that information to make it easier to set repeat angles on a given knife (with a given stone reference) using the blade table to zero, instead of trying to zero on the knife itself each time.
Now for the fun part
I think Rick's question and analysis is spot on from a purely geometric/mathematical point of view. If you had an imaginary knife with a pure wedge shape of let's say 4 degrees from spine to edge as Rick suggested in his example then...I agree with Rick that true angle of the EP to a particular point on the blade edge when sharpening, based on the blade center line would be an offset of 2 degrees, or half the measured offset.
I think the water gets cloudy, though, when we get in the real world of knife geometry with non-50/50 side grinds and convexing, etc. making exact measurements difficult, depending on how the blade is held to the table, and if it's held consistently throughout the sharpening process, from session to session. An to make it even more interesting, the angle will change with the distance that the blade edge is hanging over the end of the blade table, further away (bigger knife or more overhang) = shallower angle and vice versa.
My conclusion is that if you're trying to match an existing bevel, or you're just sharpening to an approximate angle that works for your intended purpose, Madrookie's method makes perfect sense and is easier to execute. If the bevel works for that knife, it really doesn't matter if, say, a measured angle is 15 degrees, but the true angle to centerline is 13 degrees. Also, if the knife is not perfectly symmetrically ground on each side, in a manner that translates into consistency on the EP, then the true angle of the bevel on each side to the blade center line will vary a bit.
If your intention is to truly set a bevel that is exactly, say, 15 degrees to the knife center line - and if the knife blade is pretty symmetrical, then I'd say, yes half the offset and move the rod/stone angle up by that amount in addition to the 15 degrees. In the above example - 17 degrees.
IMO you can also help repeatability and consistency by keeping your blade edges positioned to a similar amount of overhang off the blade table edge - both from knife to knife and session to session.
Damn - my head hurts now! Two things keep swirling in my head:
That song "Kung Fu Fightin'" and Eddie Murphy saying: "GI Joe with the Kung Fu grip" in Trading Places.