I didn't read every post so this may have been covered. The actual angle on the edge can change depending on how the edge is positioned on the blade table. One good example is if sharpening a pocket knife with a saber grind. If the blade tang is flat on the table the edge will bit higher off the table even if it is right at the edge of the table. This lowers the angle. Or when the edge is farther off the end of the table the angle is lowered also. So no matter where the marks are on the rod or what the actual angle is when the stone is resting on the knife edge there needs to be some constant IMO. To create this constant to my liking I bought some 5/16" rod at Lowe's and made my own vertical rod for the EP. I then put a tape blank in the EP and rested it on the end of the blade table. The tape blanks are 1/8" thick just like a stone sold with the EP. There is nothing magical about this thickness, it's just a standard. With this 1/8" inch standard I then used my angle cube to set the angles at every degree from 10 dps to 20 dps and put a mark on the rod using a Dremel and a thin cut metal cutting disk. Now I knew how to set the EP for a knife edge resting right on the end of the blade table. This is the constant. Then comes any inconsistancy created by the actual position of where the edge is regarding the end of the blade table and how thick each stone is.
No matter how each person does it everyone will establish their use of the EP to get whatever accuracy they desire. I figure the only way to know the exact (almost) angle you create on an edge is to put your stone on the EP then sit the stone on the knife edge as it rests on the blade table then adjust the EP angle using the angle cube. I found this procedure to be too difficult to accomplish. I also believe there will be no difference in cutting with an edge created at 15 dps and the edge at a 16 dps. If the edge at these two angles is evaluated in a laboratory there may be some cutting difference but for everyday use I doubt if anyone could be able to tell the difference. I don't think I could.
The exact angle on an edge is not the greatest benefit of the EP IMO. It is the consistant angle stroke and repeatability that it brings. Keep a list of knives and angles on those knives to set the correct angle for the next touch up. This will take most of the guess work out of maintaining your edges. Good luck.
If you are new to sharpening and/or using the EP this is what I believe to be the overall best way to sharpen a knife for performance and ease of daily maintenance. Put a single bevel on the edge as low as possible. I like 12 dps. Sharpen until the edge apexes (both sides meet to create a sharp edge). Use the knife. When it needs a touch up set the EP to 15 or 16 dps and perform 2 or 3 very light strokes per side SWITCHING SIDES AFTER EACH STROKE. Switching sides every stroke will minimize burrs. Then perform one VERY light stroke per side to eliminate any very tiny burrs. I use more of a push/sliding stroke for this burr removing stroke. Also, you can reduce the amount of pressure on the edge buy using only the end of the stone closest to the handle. The opposite end of the stone puts more pressure on the edge due to the weight of the stone, This is a slight amount of pressure difference that may or may not have any effect.