Didn't actually expect a reply! Glad you're still around :)
I just reread the entire thread and now remember what you sought exactly. What I've added (in v0.5.8-alpha.1) is the possibility to use either/both the Manual and Automatic mode to have several windows (max 3 for performance reasons) running at the same time. The Automatic mode works just like before, so it will stay in place, remove the text and then display the text in-place.
I do understand, from reading this thread completely, that what you ideally would want is a completely separate panel where the translations show up automatically after selecting an area to translate. This does unfortunately still not exist. However, despite my negative outlook on this type of feature several months prior, I'd say I'm convinced and have changed my mind about it. There are indeed use cases for this, and I would like to add this type of translation window as well. I promise I will have a look at it, but I'm in the middle of prepping for a Steam release so it may not come within the next few weeks. We'll see.
Until then - I recommend you to go to the 'General' tab;
1. Disable "Show automatic border"
2. Enable "Locked window"
3. Enable "Click through"
These settings should help make the "Automatic" mode less disturbing to the gameplay experience.
Do have a look in the Keybindings section a well, as there are several keys there to make things more modular when in-game.