Keynote has some settings in its settings that also need to be set. Try the following:
/usr/bin/defaults write com.apple.iWork.Keynote PresentationModePlayWellWithOthers 1 /usr/bin/defaults write com.apple.iWork.Keynote MouseVisibility 2
Definitely required 1st. The second is just for practicality.
This is in addition to what Rob suggested above, setting the window level just above the NSScreenSaverWindowLevel level.
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