I am using Mathematica in Linux (Manjaro and CentOS) with the XFCE desktop environment. Within XFCE, there is a setting that clicking within a window, or bringing it to focus, will not raise the window on top of other windows.
There is however an issue with some applications that draw their own windows, instead of using the XFWM, such that clicking anywhere inside the window or bringing it to focus will also raise it. Chromium and Brave Browsers have the same issue, but they have an option to "Use system title bar and borders", which allows XFWM to draw the window such that the raise window settings are correctly applied.
Now, what I am wondering is, is there a setting such as this in Mathematica? I have tried out the window settings in the option explorer, but I could not find anything relevant.