Further testing without smooth-scrolling enabled suggests that it doesn't matter if smooth-scrolling off or on:
I ran elp without smooth-scrolling on again, same file: next-line 685 18.373000000 0.0268218978
Function Name Call Count Elapsed Time Average Time
============= ========== ============ ============ next-line 726 17.129000000 0.0235936639 line-move 686 16.911000000 0.0246516034
And I re-profiled with the older emacs build, same .emacs startup files:
Function Name Call Count Elapsed Time Average Time ============= ========== ============ ============ next-line 653 1.5950000000 0.0024425727 line-move 652 0.5180000000 0.0007944785