This probably makes some other tickets obsolete and clairfies some others.
I have finally figured out how the tree and selection operate.
To make the language easier assume the root of the tree is at the top and the leaves are at the bottom.
If you select/enable any node then that selects and enables every node from that point down to and including the leaves. If you unselect a leaf or sub branch and then write the chains I expected the unselection to be preserved and that expectation caused much complaint and confusion.
If I want to un select a sub tree then I need to do it as close to a leaf as possible and then make sure nothing above is selected.
If I don't want to do the war as a hippy then I unselect it, unselect the parent Isle War and unselect Main.
Now that I have figured this out I am much happier about how the tasks I don't care about are hidden.
But there are some tasks that are enabled only when Main is selected that are logical prerequisites. Level Up and setting the ballroom song are two such tasks. When the Hidden City is available to open seems to interact with the selection of Main and tasks to make the Island available don't always appear.
Toggling Main will identify what tasks might need to be elsewhere.
If I had to address this I might make a new category, one level down from the root, call it Misc and make sure any task that is not already listed as a prerequisite is a leaf under Misc.