I'm new to this game, and starting to switch off the automated features, but I noticed that if I switch off automation on research it still picks research options for me, i.e., it won't let me research nothing. Okay, why would I want to research nothing? Nevertheless, I still wonder whether I'm missing something. Is there anything you can do to prevent research being picked automatically? Also, does it do the same thing with any other automated features?
I think you are referring to what happens when you first start a game. Research projects are automatically selected for the first 2-3 weeks before you take over control. To deselect them right click then left click to select another.
Basically you are right in that the first couple of weeks of the game research runs automatically regardless of the setting. After that intial period full manual control is in your hands, including the decision to change research projects or not.
Oh, and I think you can research nothing by deselecting all research projects.