I must admit I am not convinced with your argument and would much prefer an Applescript solution.
( Which if we had I am pretty sure Applescriptors like my self would offer up code)
But a suggestion (simplified ) of how the Hype team may do this is to offer a new type of Group.
These groups would be called Advanced Export Groups.
If you create a Advanced Export Group, a new Advanced Export Group icon appears at the top of the element tree.
Advanced Export Groups will always be at the Top of the element tree.
Elements added to a Advanced Export Group do not show as moved in the element tree. This is because we do not want to change the layer index. But opening an Advanced Export Group will reveal a reference to any elements added to it.
Advanced Export Groups could also have the hidden/display eye next to it.
If set to hide, all referenced elements would be hidden. Overriding the original elements hidden/display.
If set to display then the referenced elements original setting is honoured, which would be either hidden or display
When using Advanced Export, the Advanced Export Groups will be listed with a check box to include or not include.