As far as any% is concerned, the only difference glitch-wise is that non-JP versions allow you to do fruit storage, which makes EYG both easier and faster, since you don't have to make the Stus attack you in order to dismount Yoshi and throw the papaya through the gate. The physics of ejecting off of Yoshi are also different on JP, meaning that you can do a slightly faster strat at the end of Ricco 8 in 79 and 96 shines. You can also do a version of Gelato Skip in Episode 6 with Yoshi for Hoverless and No Major Skips on JP that saves a small amount of time over doing Gelato 6 normally.

In Pianta Episode 1 you can do a roll out hover spray coming out of a water slide to grab the Chain Chomplets in JP which is a little more faster. This method doesn't work in ntscu and pal, you have to do regular spam sprays to be able to grab them which is a little slow coming out of a water slide.

I'm bumping this because this exists: https://www.speedrun.com/sms/guide/o7a51

There's a number of other small differences not listed.