The game uses RPGMaker MV as an "engine", but has quite a few additional portions in various javascript plugins and the like. Some things are just...incredibly well-hidden, too. Additionally, some text is also hard-baked into the image files. For the images, I do the translation for those, but it's someone else who actually edits the images. What all that adds up to is that it's the game's base files that get translated in order to make the English-release version. When it's ready, the expansion will be released officially as a complete product, just like the base game was (note: for a given value of "complete". AFAIK, the expansion will still require the base game to be purchased separately).
Per Ci-en, SQDT is planning to use RPGMaker MZ for the sequel, but assuming circumstances don't change between now and then, that probably won't change the general process of the translation in a big way, at least.