With the most recent check-in [7ea0be3c] to the bugfix branch, if you uncomment
the second of these three lines:

<verbatim>
	# To make things even worse on TkAqua, uncomment this line
	# wm overrideredirect .balloon 1
	wm withdraw .balloon
</verbatim>

then I think you will find that the help balloons work fine in FullScreen mode.

Do you have a test script that shows the issue with transient windows?