Basically just a restatement of what Crafft said, but the distance between the support point of the rod attached to the stone and the contact point between the stone and the knife, has to stay reasonably uniform. As that distance changes, so does the angle at which the stone encounters the blade.
There is a very slight change as you advance the stone along the straight portion of the blade without moving the knife. The change tends to be greater near the tip though, because it becomes increasingly difficult to support the knife while moving its handle away from the stone. You could easily calculate this with basic trig functions to get an idea of the rate of change as a function of the secondary bevels total angle.
Another factor is that the primary grinds near the tip of a knife are sometimes at a different angle than those at the straight portion of the knife.
So, you have to keep a close eye on the relationship between the primary bevel and your new secondary bevel - assuming you want that relationship to remain constant. If the primary bevel's angle is changing, then you have to change along with it. If the primary's angle is not changing, but the geometry of your set-up is, then you have to compensate. It also may be that both are changing.
The Edge Pro is a highly effective tool, but it is not fool-proof. It does not eliminate the need for some degree of manual skill and visual reference... just gives you fixed reference points at the blade and stone supports to work with.
As you move away from sharpening a knife with a simple, constant cross-section on the Edge Pro, the quality of your results will depend on how seamlessly you can follow the geometric change. Relative to free-hand sharpening, the Edge Pro makes it a lot easier to follow a consistent angle, so it can be a little more difficult to keep up with any transitions that are needed.
