Based on current known route/strats, I found the JP version is faster than the US version due to the Smiley Navel fight in Memory Cave - this boss takes one less hit/cycle saving ~15 seconds.

I didn't realize there were already forum posts for this game and came here to post the same information. I recently started running this game (already own the NA version) and could not figure out why I was losing so much time on my Memory Cave splits until watching the posted runs on the JP version more closely.

I've noticed the NA version has the advantage of being able to skip the text at the end of bonus games, saving ~3-4 seconds, but given that you only intentionally do 1 bonus game on the route this doesn't come close to making up for the loss on the Smiley Navel fight... Oh well, I'll probably still see how good of a time I can get on the NA version since I already own it anyways...

I'd be interested to know if any other version differences are found!

Circling back to this now that strats have changed, the JP version no longer has a significant time save over the US version. The Smiley Navel fight time is the same in both versions now, although the strat for the US version is slightly harder to execute than JP version.

Right now, the US version is slightly faster because of the bonus text skip and the one enemy in Memory Cave that can be defeated with one hit. However, being forced into the crab before the 2nd auto-scroller is not guaranteed in the US version.