The diopter merely puts in-focus or out-of-focus the contents of the viewfinder...the LCD text as well as the image formed on the focusing screen.
Take the lens off the camera and refocus the diopter so that you can best see the a) focus points and the b) center circle (spot area) and the c) in-viewfinder control status displays. All THREE need to be 'in focus' simultaneously, or you have an internal issue with alignment of the focus screen with the SI plate with the control status LCD.
Then put the lens back on, and see how Live View focus coicides (or not) with the viewfinder image of the image on the focus screen.
Okay, I just did that. At the same diopter setting I have been using (down 5 clicks), all three are in focus and tack sharp in the viewfinder.
I focused with auto focus, checked the LCD and it's tack sharp (looks a little blurry through viewfinder.
Next I focused manually so the image in the viewfinder was TACK SHARP. I switched to the LCD and zoomed in - completely blurry.
The LCD and the viewfinder (image on the focus screen) do not coincide at all.