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It is not a mystery, and has nothing to do with Geany. I have the identical issue, and have been researching and studying the topic for months. I am also using Kubuntu 22.04.2, and its GTK/Gnome relative, Linux Mint Cinnamon 21.2.
The initial focus acquiring behavior was taken over by the window one is working in. In this context, the desktop is counted as a window. This also applies to opening Firefox where the home page is DuckDuckGo.
Running Geany, or any other software, from a .sh file, is the only quick solution I can think of. This would set the focus after Geany is open. 'xdotool click window = activetitle_ 1'. I haven't tried this particular code but most of my apps' .desktop files use .sh files to accommodate shell commands before or after starting an app.
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