To be brutally honest, that is one aspect of this game I do not like: Needing to research UI (User Interface) items, not related to game play. Would you want to play a game that, for example, only ran in 640x480x8 resolution, unless you researched "Higher Resolution and Color Depth" in-game? Only items that might be part of both should be an in-game research-able item (for example, being able to research build/production queues could be both a UI thing AND an in-game thing.) These are the kind of issues which caused me to stop playing the game at all. I want to come home, relax, and enjoy a game after a hard day at work--If I wanted to be stressed and frustrated, I'd stay at work, where they PAY me for it.
Yeah indeed, we need to do some changes here, at the very least with some of the most commonly annoying things most users would want to choose settings.
However, scrapping some sort of automation options through the gameplay we don't want to scrap, as they can feel very rewarding for the player to reach and at the "right time". Even some QoL options (the right ones) can fit this model really well - of course some like "ignore popups"/"don't pause during popups" should be available always, but I think some current and potential new ones could fit very well under research still.
I think you put it nicely - if something can be frustrating, it should be a setting by default. If something improves on something/makes it easier/automated it should in most cases be fine (and potentially even better!) to be part of research.