If I understand your proposal, the currently invisible tools are at the top
of the list (in bold), in the left-to-right order in which they would appear if
you resized the window much wider.  The currently visible tools would be
below the invisible tools in the list (not in bold) and would also appear
in the left-to-right order in which they appear in the window.

That's not bad.  I think you should perhaps implement that, if possible.
Only user experience with 6.0 will tell whether that is the best choice.
Ultimately, users might ask for a preference that determines the order of
items in a Show List popup.  In addition to the one you are suggesting 
(and I am recommending you implement for 6.0), one could also imagine
an ordering sorted by name either before or after sorting by visible/invisible
status.  I guess the possibilities are endless and the best choice may depend
on how the user finds the right tool (by position within the list or looking
at the names and expecting them to be sorted).