Sorry for being a little bit late to this thread.
The change in DOM ordering is intentional to help improve accessibility, especially on iOS. Relying on how Hype internally modifies and represents the DOM isn't officially supported because we need to reserve the right to make changes here.
That said, we did include a small valve for projects that might need the old method. You can use this Terminal command for the DOM layout to match the z-ordering:
defaults write com.tumult.Hype2 elementInsertionOrderSortMethod "compareByZOrdering:"
If you need to use the new default method of ordering by top/left, then you can revert via:
defaults delete com.tumult.Hype2 elementInsertionOrderSortMethod