I plan to rewrite translation tool, when Godot 4.1 gets released (in few weeks), so I can incorporate some of the requested changes, but note that it's written in game engine so there are not many advanced text functions I could use to implement requested features and I'm not going to throw too much time on this project.
The tool must stay simple to use for even the dumbest users so I'm not planning to do anything too complicated for users to comprehend. That said it is not tool you should use to professionally translate the game. If you want to join official translation effort to English, then contact eccma or mods in LonaRPG discord.
Google is constantly making changes to their translator so there is every few months they do that breaks some workflow. Originally it was possible to upload whole txt file to google translate and download translated version of it. But they removed that ability and allowed only more complicated text file formats I can't reasonably create in Godot.
I think you've missed two warnings in the tool that declares the tool overrides MTL folder every time directory is selected.