How do you change the location of the FPS counter in World of Warcraft?

Tricky, but possible.

The FPS display is no normal UI element. It's a simple Label ("FPS") and Text (the number as a String). That's probably why you have issues with its positioning (and some addons may not find it).

So...

1. Use the MoveAnything addon. Look for Framerate and you should be able to move it around. It used to work, but I can't confirm it for BfA.

2. Use a macro to toggle it and move it to a specific position:

Code:

 /run FramerateLabel:ClearAllPoints() FramerateText:ClearAllPoints()
 FramerateLabel:SetPoint("RIGHT",UIParent,"CENTER",X,Y)
 FramerateText:SetPoint("LEFT",FramerateLabel,"RIGHT")
 ToggleFramerate()

X and Y are the coordinates relatively to the center of your screen. Negative values go left/down and the positive ones up/right:

   Y
-X C X
  -Y