When I popup kmail from the tray icon, I get switched to the desktop that kmail was on before I minimized it to the tray. That's quite disturbing. I need the window to pop up right on top of what I'm doing right now.
It's even more disturbing when there's some random popup window from some random application on another desktop. Then I get moved to that desktop without warning .

So, what I think is needed, is an option to disable automatic desktop switching, which does the following:
1. New Main Windows are always opened on the current desktop
2. Urgent popups from an app on another desktop don't cause a switch, but instead highlight their taskbar entry and cause the task bar to be shown if it's hidden.

Why has this been moved to Office & Productivity? This is not about kmail or any other app, it's about Window Management.

As far as I am aware this behaviour ( automatic desktop switching ) cannot be disabled.

Have you tried increasing the focus-stealing prevention level? Also, there is an option in the advanced window settings for "Hide utility windows for inactive applications", this may do it. Those are my settings, and I never see what you are seeing, so it may (or may not) help.