I have set my Windows taskbar to autohide. When you move the mouse to the bottom of the screen, the taskbar will appear and allow you to click on the start button, etc. The taskbar appears above all other windows.
SourceTree is the only application that I use that ignores this feature. If I maximize SourceTree's window and bring my mouse to the bottom of the screen, my taskbar is not visible. It will only become visible if I resize the window or switch to another application.
I have reproduced this issue on multiple computers. This is not a result of a Windows setting. There is no setting to change the taskbar's "always on top" feature in Windows 10. The default is "always on top" and SourceTree overrides this.