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