I've been playing the 360 port a lot this past week. I'll play it right after or right before MFBL God Mode (360), which I've set to 1 frame of lag (the PCB has 2). And I play SDOJ in tate with smoothing ON (no extra windows). I can't feel any difference in lag between SDOJ and MFBL. I thought there was less with smoothing off, and maybe there is a tiny amount, but I can't really feel a difference in a run (I guess I didn't test it enough before when I claimed there was a noticeable difference). Smoothing ON looks so much better on my monitor, so I'll stick with that. Keep in mind my Dell U2414H monitor has 4ms of total input lag, which is nearly CRT-level.
I wonder if the input lag was mainly a problem before the patch. I know several things were messed up pre-patch, including the extra windows causing slowdown in the game.
On a different note, I think it would be great to have a "black label" of this game released on the eXA hardware with the graphics and sound of the X360 version, with various BL tweaks added. For example, it would be cool to have a 2-loop version of this game, with only one ship type available (Expert type).