The timings in ing's post look accurate, but he didn't mention some places where the Japanese version loses time. Since you can't hit the Great Bay Owl without Zora Mask in the Japanese version, you have to swim out to sea twice. The lack of Flying Zora also complicates the bomb route, since you have to use explosives to hover to the Great Bay Fairy Fountain. Having to swing your sword to use ISG whenever you enter a new area barely costs time in the short term, but probably adds up to about three or so seconds over the course of the run.
All of these factors, combined with the lack of Turtle CS Skip (which I
made a video of, not realizing that ing had done the same), means that the Japanese version is likely to be slightly slower than the US version. The magnitude of difference is not the same as in OoT, though; we're talking somewhere in the realm of seconds, not minutes.