Put a pin icon on the helper windows (view > windows) in FME Desktop. When pinned the window stays open (as it is the behaviour now all windows are pinned); when not pinned the window auto hides if you have not moused over it for say 5-10 seconds (configurable in settings?). The window hides to a narrow side bar, when you mouse over / click the sidebar, it opens back out.
Collapsible / Pinable Windows
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