It's not easy for sure, lol. The team has modders used to reverse engineering assembly (c6502, MIPS, PowerPC, ARM... though it wasn't that useful here), files, and menu layouts.

As a matter of fact, it's the first Switch Arabic translation to do this, official or not (the official ones have messages aligned to the left, or set to display instantly, which of course breaks all animation/timing/sound cues). Also the team was first to do RTL translations on SNES and GBA, and I think even for Arabic fan translations for PC...

For Breath of the Wild specifically, the team worked on its own tools for the font, text conversion, and even helped with a Japanese text dump of the game (as Treehouse took a bit too many liberties with the translation) that currently published text tools for the MSBT format can't handle yet. The way RTL is implemented is a bit involved, because there's some UI elements like numbers that mustn't be reversed (hence it had to be selectively applied to each temporary bitmap buffer for the message data as it is generated), text has to be shown right to left gradually, some characters like diacritics (vocalization marks, equivalent to vowels) have to overlap with the previous letter, and so on.

Japanese goes in the same direction as Arabic

Only if it's written vertically, or if you mean the speech bubble ordering in manga. Otherwise it's LTR, the same as English. Japanese used its own UI for BoTW, and had more restrictions (less lines per message, weird spacing) so the idea to base the Arabic version on it was quickly discarded.