I got my Switch from the Americas, but my Switch language and region is set to Japan.

The Region/Language your switch is set to makes no difference when it comes to speedrunning. The only difference is what the game's language is set to, in which case Japanese is the fastest. You can also change the Language/Region at any point by going into system settings. (Click the gear icon on the home menu, bottom on the settings menu selection bar to the left, then the second item with green text on the right)

Yes, but I mean, when you submit a run, you have to put the region of your Switch. I'm asking if it would be Japan, or the Americas.

It would be what region you have it set to. If the region is set to Japan, then it's Japan

Okay, thanks!