If anyone has info on how to solve this issue it would go a long way in me being able to provide (Hopefully half-decent) translations to the community.
I'd recommend using Sugoi instead of DeepL. If your translation software is T++, then I'd recommend the RedSugoi plugin. Ideally you'll want to use the 3.3 or Levi model of Sugoi, in the offline server configuration. You won't have any duplication issues with Sugoi, and it's also much less likely at missing text - something I've observed happening frequently with DeepL, that it ignores lines of dialogue, ending up in an incomplete translation.
The translation quality is heaps better than Google or Bing, and 95% of the time better than DeepL as well. Another upside: As you can host Sugoi servers locally (offline servers), you can achieve translation speeds of more than 1000 characters / second even on an older PC (I only have hardware from 2014 for example). This means you can save a huge amount of time for manual edits later on, as the MTL process itself will be done in a matter of minutes even for big games.
The biggest hurdle for Sugoi are pronouns. While the translation is otherwise surprisingly accurate and rarely even requires manual edits, "pronoun-scrambling" remains an issue (he/she/me/they etc).