I don't know if it's possible to combine NT with Reunion without doing it manually. Too many elements from encounter tables to game scripts are likely different; too different for a tool to be able to patch them together cleanly because it won't know what to keep and what to overwrite.
Here's an example, Oleary mentioned NT's Beginner's Hall. A lot of the tutorials there in the default game, I find, are completely redundant. They cover things like how to Save your game, and worse than that a chunk of them are delivered in the slow-ass Menu tutorial format. So for NT, I changed all of these to explain game mechanics that cover things I usually got asked during my challenge runs, etc. Things like how damage mitigation from Sadness/Back-Row works, ATB settings and their advantages/drawbacks, how Natural Dex vs. Boosted Dex works; stuff like that. I also turned them into normal text boxes, instead of Menu tutorials. The other tutorials that do use normal text boxes in the default game were changed too; and some of the explanations, like for elements vs. enemy types in NT, needed an extra box or two.
Now our tool comes along with Reunion text & scripts to inject. First off, the triggers for the Menu tutorials are gone so that translated text is lost already, except it'll translate the names of the tutorial options themselves which means when you pick, say, the explanation on Saving you'll get the extra NT text talking about ATB settings instead. The other tutorials will be worse; if there's additional text boxes, then you'll get the translated text followed by an extra text box or two from NT that's talking about something else entirely; in short, it won't make a lot of sense.
I think that'd generally be the problem; just a disconnect between what the mods do. Reunion translates the text, NT repurposes it instead. There's going to be a lot of overlap that only a manual edit can navigate cleanly.
