As @Tavikron said, anytime you want to make a Union that has to have a certain Orientation, even if has a lot of Unions, Parts or Negated items, always click first on the item you want the Orientation of the final Union to go by.
It’s similar to if you want to use the Move tool to move a selection of Parts together, except you have to select them in reverse order, because the last item selected will align the Orientation of the Move arrows with that item.
Other posts about this:
<Can you change the orientation of the selection box on a union
<https://devforum.roblox.com/t/how-do-i-change-the-front-face-of-a-union/57041