ediff-control-frame-upward-shift

ediff-control-frame-upward-shift is a variable defined in `ediff-wind.el'.
Its value is

42

Documentation:
The upward shift of control frame from the top of buffer A's frame.
Measured in pixels.
This is used by the default control frame positioning function,
`ediff-make-frame-position'. This variable is provided for easy
customization of the default control frame positioning.

You can customize this variable.