AFAICT, this is because the function that was introduced to de-duplicate
the horizontal line code does

(let ((p (point)))
  (insert "\n")
  …)

whereas the code to draw the last line did:

(let ((p (1+ (point))))
  (insert "\n\n")
  …)

If I'm not mistaken, this can be fixed simply by adding (insert "\n")
before the final call to custom-group--draw-horizontal-line, as done in
this patch: